Starting phenix.real_space_refine on Thu Aug 6 05:55:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ux7_64575/08_2026/9ux7_64575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ux7_64575/08_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_64575/08_2026/9ux7_64575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ux7_64575/08_2026/9ux7_64575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ux7_64575/08_2026/9ux7_64575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ux7_64575/08_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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13495 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4682 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 555} Chain: "B" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4682 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 555} Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2456 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "D" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 836 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 839 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Time building chain proxies: 2.84, 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: 1.16 Conformation dependent library (CDL) restraints added in 561.6 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 61.2% alpha, 9.5% beta 37 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.67 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: 2.72 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3832 1.34 - 1.46: 2511 1.46 - 1.57: 7312 1.57 - 1.69: 160 1.69 - 1.81: 68 Bond restraints: 13883 Sorted by residual: bond pdb=" C3' DG D 18 " pdb=" C2' DG D 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.89e+00 bond pdb=" C3' DT D 8 " pdb=" C2' DT D 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.85e+00 bond pdb=" C3' DT E 39 " pdb=" C2' DT E 39 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.47e+00 bond pdb=" C3' DT E 43 " pdb=" C2' DT E 43 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.99e+00 bond pdb=" C3' DA E 38 " pdb=" C2' DA E 38 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.91e+00 ... (remaining 13878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 18306 1.77 - 3.55: 626 3.55 - 5.32: 81 5.32 - 7.09: 16 7.09 - 8.86: 3 Bond angle restraints: 19032 Sorted by residual: angle pdb=" N LEU C 115 " pdb=" CA LEU C 115 " pdb=" C LEU C 115 " ideal model delta sigma weight residual 113.97 107.61 6.36 1.28e+00 6.10e-01 2.47e+01 angle pdb=" C SER A 304 " pdb=" CA SER A 304 " pdb=" CB SER A 304 " ideal model delta sigma weight residual 115.79 110.44 5.35 1.19e+00 7.06e-01 2.02e+01 angle pdb=" N3 DT D 22 " pdb=" C4 DT D 22 " pdb=" O4 DT D 22 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E 36 " pdb=" C4 DT E 36 " pdb=" O4 DT E 36 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT E 53 " pdb=" C4 DT E 53 " pdb=" O4 DT E 53 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7074 17.88 - 35.77: 827 35.77 - 53.65: 351 53.65 - 71.54: 68 71.54 - 89.42: 25 Dihedral angle restraints: 8345 sinusoidal: 4065 harmonic: 4280 Sorted by residual: dihedral pdb=" CA THR B 357 " pdb=" C THR B 357 " pdb=" N ILE B 358 " pdb=" CA ILE B 358 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLU C 300 " pdb=" C GLU C 300 " pdb=" N LEU C 301 " pdb=" CA LEU C 301 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL A 533 " pdb=" C VAL A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 8342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1586 0.045 - 0.089: 423 0.089 - 0.134: 131 0.134 - 0.179: 10 0.179 - 0.223: 1 Chirality restraints: 2151 Sorted by residual: chirality pdb=" CB ILE C 253 " pdb=" CA ILE C 253 " pdb=" CG1 ILE C 253 " pdb=" CG2 ILE C 253 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 484 " pdb=" N ILE B 484 " pdb=" C ILE B 484 " pdb=" CB ILE B 484 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ASN B 170 " pdb=" N ASN B 170 " pdb=" C ASN B 170 " pdb=" CB ASN B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 2148 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 362 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C VAL B 362 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL B 362 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS B 363 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 363 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C LYS B 363 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS B 363 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 364 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 484 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 485 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " -0.030 5.00e-02 4.00e+02 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 261 2.67 - 3.23: 13181 3.23 - 3.78: 22646 3.78 - 4.34: 29813 4.34 - 4.90: 46704 Nonbonded interactions: 112605 Sorted by model distance: nonbonded pdb=" OH TYR B 45 " pdb=" O PRO B 485 " model vdw 2.110 3.040 nonbonded pdb=" O LYS B 98 " pdb=" OG SER B 101 " model vdw 2.127 3.040 nonbonded pdb=" NZ LYS B 98 " pdb=" OE2 GLU B 102 " model vdw 2.136 3.120 nonbonded pdb=" O ALA C 101 " pdb=" OG1 THR C 104 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASN B 305 " pdb=" NH1 ARG C 180 " model vdw 2.192 3.120 ... (remaining 112600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13883 Z= 0.308 Angle : 0.728 8.864 19032 Z= 0.492 Chirality : 0.045 0.223 2151 Planarity : 0.004 0.055 2125 Dihedral : 18.586 89.424 5555 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.01 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.23), residues: 1422 helix: 1.86 (0.19), residues: 776 sheet: 0.75 (0.41), residues: 160 loop : -1.23 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 477 TYR 0.024 0.001 TYR B 479 PHE 0.024 0.002 PHE A 532 TRP 0.020 0.002 TRP C 98 HIS 0.008 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.31 (13883) covalent geometry : angle 0.72800 / 0.49 (19032) hydrogen bonds : bond 0.17043 / 11.38 ( 819) hydrogen bonds : angle 6.30856 / 4.45 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.445 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: 0.1142 time to fit residues: 34.4028 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 : 0.512 ------------------------------------------------------------------------------- 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: 40.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 ASN B 105 GLN B 236 GLN B 237 ASN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.169048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.116340 restraints weight = 28393.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116778 restraints weight = 18026.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.116746 restraints weight = 11948.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117572 restraints weight = 12020.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117567 restraints weight = 11006.577| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13883 Z= 0.238 Angle : 0.702 10.830 19032 Z= 0.389 Chirality : 0.046 0.225 2151 Planarity : 0.004 0.042 2125 Dihedral : 19.611 59.967 2436 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.29 % Favored : 95.43 % Rotamer: Outliers : 1.03 % Allowed : 9.90 % Favored : 89.07 % 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: 1.16 (0.22), residues: 1422 helix: 1.89 (0.18), residues: 808 sheet: 0.31 (0.39), residues: 166 loop : -1.16 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 180 TYR 0.034 0.002 TYR B 45 PHE 0.020 0.002 PHE B 558 TRP 0.017 0.002 TRP A 142 HIS 0.005 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 (13883) covalent geometry : angle 0.70216 / 0.39 (19032) hydrogen bonds : bond 0.05279 / 3.41 ( 819) hydrogen bonds : angle 4.69407 / 3.32 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8134 (m-80) cc_final: 0.7858 (m-80) REVERT: B 82 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 347 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8202 (tpm170) REVERT: B 463 LYS cc_start: 0.8709 (mppt) cc_final: 0.8471 (mmtt) REVERT: C 43 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5559 (mt-10) outliers start: 14 outliers final: 6 residues processed: 165 average time/residue: 0.1067 time to fit residues: 26.6769 Evaluate side-chains 128 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 146 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 145 optimal weight: 50.0000 chunk 81 optimal weight: 2.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 462 ASN ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 HIS C 126 GLN C 147 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.163078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.110272 restraints weight = 30363.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109654 restraints weight = 20079.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110022 restraints weight = 13574.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.110716 restraints weight = 12300.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110881 restraints weight = 11374.170| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 13883 Z= 0.341 Angle : 0.761 11.465 19032 Z= 0.406 Chirality : 0.047 0.341 2151 Planarity : 0.004 0.052 2125 Dihedral : 20.170 59.884 2436 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.92 % Favored : 94.80 % Rotamer: Outliers : 2.58 % Allowed : 11.67 % Favored : 85.75 % 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: 0.86 (0.22), residues: 1422 helix: 1.65 (0.18), residues: 811 sheet: -0.06 (0.42), residues: 149 loop : -1.16 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 277 TYR 0.045 0.002 TYR B 287 PHE 0.018 0.002 PHE A 532 TRP 0.014 0.002 TRP A 103 HIS 0.007 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.34 (13883) covalent geometry : angle 0.76127 / 0.41 (19032) hydrogen bonds : bond 0.05577 / 3.62 ( 819) hydrogen bonds : angle 4.73510 / 3.37 ( 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 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8137 (m-80) cc_final: 0.7833 (m-80) REVERT: A 251 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.7969 (mt) REVERT: B 64 MET cc_start: 0.8429 (mmm) cc_final: 0.8146 (mmm) REVERT: B 82 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8183 (tm-30) REVERT: B 283 THR cc_start: 0.7523 (p) cc_final: 0.7233 (p) REVERT: B 331 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7237 (t80) REVERT: B 347 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8231 (tpm170) REVERT: B 407 GLU cc_start: 0.9066 (tp30) cc_final: 0.8806 (tp30) REVERT: B 415 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8247 (mtp-110) REVERT: B 459 MET cc_start: 0.8373 (tpt) cc_final: 0.7835 (tpp) outliers start: 35 outliers final: 21 residues processed: 164 average time/residue: 0.1052 time to fit residues: 26.2972 Evaluate side-chains 145 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 242 MET 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 299 THR Chi-restraints excluded: chain C residue 309 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.0010 chunk 107 optimal weight: 0.0970 chunk 47 optimal weight: 30.0000 chunk 95 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 ASN B 236 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN 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 = 0.165410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.111994 restraints weight = 29564.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112761 restraints weight = 17333.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113398 restraints weight = 11203.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.114187 restraints weight = 10879.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114017 restraints weight = 9803.735| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13883 Z= 0.142 Angle : 0.619 12.857 19032 Z= 0.338 Chirality : 0.043 0.314 2151 Planarity : 0.003 0.039 2125 Dihedral : 20.247 59.967 2436 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.85 % Rotamer: Outliers : 2.07 % Allowed : 13.37 % Favored : 84.56 % 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: 1.14 (0.23), residues: 1422 helix: 1.95 (0.18), residues: 803 sheet: -0.19 (0.40), residues: 163 loop : -1.05 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 277 TYR 0.034 0.002 TYR B 45 PHE 0.017 0.001 PHE B 11 TRP 0.010 0.001 TRP A 103 HIS 0.006 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (13883) covalent geometry : angle 0.61858 / 0.34 (19032) hydrogen bonds : bond 0.04565 / 2.96 ( 819) hydrogen bonds : angle 4.45786 / 3.18 ( 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 179 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8399 (m-80) cc_final: 0.8057 (m-80) REVERT: A 251 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7485 (mt) REVERT: B 64 MET cc_start: 0.8291 (mmm) cc_final: 0.7445 (mmm) REVERT: B 82 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8258 (tm-30) REVERT: B 331 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 347 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8171 (tpm170) REVERT: B 407 GLU cc_start: 0.9022 (tp30) cc_final: 0.8701 (tp30) REVERT: B 415 ARG cc_start: 0.8569 (mtp85) cc_final: 0.8247 (mtp-110) REVERT: C 190 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7994 (tt) outliers start: 28 outliers final: 14 residues processed: 173 average time/residue: 0.1038 time to fit residues: 27.7358 Evaluate side-chains 145 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 331 PHE Chi-restraints excluded: chain B residue 353 LYS 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 190 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 149 optimal weight: 40.0000 chunk 136 optimal weight: 0.0170 chunk 101 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN B 73 ASN B 236 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.165561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114061 restraints weight = 29912.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113184 restraints weight = 17792.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.113781 restraints weight = 12837.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114350 restraints weight = 11240.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114540 restraints weight = 10240.134| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13883 Z= 0.144 Angle : 0.599 11.706 19032 Z= 0.325 Chirality : 0.042 0.309 2151 Planarity : 0.003 0.058 2125 Dihedral : 20.261 59.570 2436 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.80 % Favored : 95.85 % Rotamer: Outliers : 2.14 % Allowed : 14.03 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.23), residues: 1422 helix: 2.06 (0.18), residues: 787 sheet: 0.22 (0.45), residues: 141 loop : -0.94 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 194 TYR 0.033 0.001 TYR B 287 PHE 0.016 0.001 PHE B 513 TRP 0.008 0.001 TRP A 103 HIS 0.010 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (13883) covalent geometry : angle 0.59899 / 0.33 (19032) hydrogen bonds : bond 0.04455 / 2.85 ( 819) hydrogen bonds : angle 4.37882 / 3.12 ( 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 173 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3731 (OUTLIER) cc_final: 0.3476 (t) REVERT: A 165 PHE cc_start: 0.8227 (m-80) cc_final: 0.8007 (m-80) REVERT: A 251 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7395 (mt) REVERT: B 35 LYS cc_start: 0.8294 (tttt) cc_final: 0.7990 (tttm) REVERT: B 64 MET cc_start: 0.8116 (mmm) cc_final: 0.7673 (mmm) REVERT: B 82 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8432 (tp40) REVERT: B 331 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.6992 (t80) REVERT: B 347 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8170 (tpm170) REVERT: B 407 GLU cc_start: 0.9024 (tp30) cc_final: 0.8665 (tp30) REVERT: B 459 MET cc_start: 0.8379 (tpt) cc_final: 0.7801 (tpp) REVERT: C 144 MET cc_start: 0.8663 (mmm) cc_final: 0.8422 (mmm) outliers start: 29 outliers final: 15 residues processed: 170 average time/residue: 0.1034 time to fit residues: 27.1923 Evaluate side-chains 148 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 ASN B 236 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** 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 = 0.4345 r_free = 0.4345 target = 0.165292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111512 restraints weight = 29764.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.111760 restraints weight = 18078.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.112826 restraints weight = 12405.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113718 restraints weight = 11189.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113740 restraints weight = 9405.305| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13883 Z= 0.149 Angle : 0.602 11.672 19032 Z= 0.326 Chirality : 0.042 0.331 2151 Planarity : 0.003 0.039 2125 Dihedral : 20.264 59.662 2436 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.73 % Favored : 95.92 % Rotamer: Outliers : 2.81 % Allowed : 13.96 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.23), residues: 1422 helix: 2.07 (0.18), residues: 793 sheet: 0.23 (0.45), residues: 141 loop : -0.92 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 415 TYR 0.033 0.002 TYR B 287 PHE 0.022 0.001 PHE B 558 TRP 0.014 0.001 TRP C 98 HIS 0.005 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (13883) covalent geometry : angle 0.60192 / 0.33 (19032) hydrogen bonds : bond 0.04368 / 2.81 ( 819) hydrogen bonds : angle 4.32716 / 3.08 ( 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 183 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3471 (OUTLIER) cc_final: 0.3202 (t) REVERT: A 165 PHE cc_start: 0.8473 (m-80) cc_final: 0.8144 (m-80) REVERT: A 251 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7413 (mt) REVERT: B 35 LYS cc_start: 0.8263 (tttt) cc_final: 0.7951 (tttm) REVERT: B 64 MET cc_start: 0.8033 (mmm) cc_final: 0.7816 (mmm) REVERT: B 237 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8987 (m-40) REVERT: B 331 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7124 (t80) REVERT: B 347 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8256 (tpm170) REVERT: B 360 ASP cc_start: 0.8741 (m-30) cc_final: 0.8502 (m-30) REVERT: B 407 GLU cc_start: 0.9046 (tp30) cc_final: 0.8684 (tp30) REVERT: B 459 MET cc_start: 0.8397 (tpt) cc_final: 0.7267 (tpp) REVERT: C 205 ASP cc_start: 0.8143 (m-30) cc_final: 0.7632 (m-30) outliers start: 38 outliers final: 17 residues processed: 177 average time/residue: 0.1041 time to fit residues: 28.5087 Evaluate side-chains 155 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU 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: 10.0000 chunk 81 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 HIS ** B 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.163589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108037 restraints weight = 29375.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107930 restraints weight = 19198.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110012 restraints weight = 13166.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.110673 restraints weight = 10044.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110541 restraints weight = 9025.436| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13883 Z= 0.207 Angle : 0.641 11.910 19032 Z= 0.343 Chirality : 0.044 0.321 2151 Planarity : 0.004 0.058 2125 Dihedral : 20.293 59.833 2436 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.22 % Favored : 95.50 % Rotamer: Outliers : 2.29 % Allowed : 15.07 % Favored : 82.64 % 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: 1.27 (0.23), residues: 1422 helix: 2.05 (0.18), residues: 786 sheet: 0.11 (0.46), residues: 141 loop : -0.93 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 415 TYR 0.032 0.002 TYR B 287 PHE 0.023 0.002 PHE B 558 TRP 0.016 0.001 TRP C 98 HIS 0.009 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (13883) covalent geometry : angle 0.64052 / 0.34 (19032) hydrogen bonds : bond 0.04542 / 2.93 ( 819) hydrogen bonds : angle 4.40920 / 3.14 ( 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 177 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3379 (OUTLIER) cc_final: 0.3113 (t) REVERT: A 165 PHE cc_start: 0.8458 (m-80) cc_final: 0.8128 (m-80) REVERT: A 177 LEU cc_start: 0.9106 (mt) cc_final: 0.8894 (pp) REVERT: A 251 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.7456 (mt) REVERT: A 356 LEU cc_start: 0.8799 (tp) cc_final: 0.8511 (tt) REVERT: B 35 LYS cc_start: 0.8250 (tttt) cc_final: 0.7914 (tttm) REVERT: B 83 LYS cc_start: 0.8573 (mttt) cc_final: 0.8206 (mttp) REVERT: B 137 ASP cc_start: 0.7998 (t0) cc_final: 0.7714 (t70) REVERT: B 331 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 332 GLU cc_start: 0.8290 (tt0) cc_final: 0.8076 (tm-30) REVERT: B 347 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8267 (tpm170) REVERT: B 360 ASP cc_start: 0.8772 (m-30) cc_final: 0.8540 (m-30) REVERT: B 368 LYS cc_start: 0.8840 (tttt) cc_final: 0.8388 (mmmt) REVERT: B 407 GLU cc_start: 0.9131 (tp30) cc_final: 0.8736 (tp30) REVERT: B 415 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8376 (mtp-110) REVERT: B 459 MET cc_start: 0.8072 (tpt) cc_final: 0.7853 (tpp) REVERT: C 205 ASP cc_start: 0.8176 (m-30) cc_final: 0.7656 (m-30) REVERT: C 256 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8395 (mp) outliers start: 31 outliers final: 20 residues processed: 170 average time/residue: 0.1089 time to fit residues: 28.3989 Evaluate side-chains 161 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 309 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 144 optimal weight: 50.0000 chunk 66 optimal weight: 0.5980 chunk 7 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 138 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.4344 r_free = 0.4344 target = 0.165199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112592 restraints weight = 29671.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112085 restraints weight = 16784.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112430 restraints weight = 11083.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113162 restraints weight = 10990.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.113268 restraints weight = 9288.267| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13883 Z= 0.137 Angle : 0.614 13.840 19032 Z= 0.326 Chirality : 0.042 0.335 2151 Planarity : 0.003 0.059 2125 Dihedral : 20.268 59.263 2436 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.85 % Rotamer: Outliers : 2.22 % Allowed : 15.95 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1422 helix: 2.08 (0.18), residues: 786 sheet: 0.04 (0.45), residues: 149 loop : -0.99 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 415 TYR 0.031 0.002 TYR B 45 PHE 0.045 0.002 PHE A 532 TRP 0.015 0.002 TRP C 98 HIS 0.004 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (13883) covalent geometry : angle 0.61364 / 0.33 (19032) hydrogen bonds : bond 0.04226 / 2.71 ( 819) hydrogen bonds : angle 4.30893 / 3.07 ( 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 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3516 (OUTLIER) cc_final: 0.3260 (t) REVERT: A 165 PHE cc_start: 0.8281 (m-80) cc_final: 0.8033 (m-80) REVERT: A 177 LEU cc_start: 0.9083 (mt) cc_final: 0.8854 (pp) REVERT: A 178 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: A 251 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7371 (mt) REVERT: A 356 LEU cc_start: 0.8747 (tp) cc_final: 0.8495 (tt) REVERT: B 35 LYS cc_start: 0.8196 (tttt) cc_final: 0.7921 (tttm) REVERT: B 331 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7166 (t80) REVERT: B 347 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8246 (tpm170) REVERT: B 368 LYS cc_start: 0.8837 (tttt) cc_final: 0.8382 (mmmt) REVERT: B 395 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 407 GLU cc_start: 0.9061 (tp30) cc_final: 0.8648 (tp30) REVERT: B 415 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8288 (mtp-110) REVERT: B 459 MET cc_start: 0.8150 (tpt) cc_final: 0.7895 (tpp) REVERT: C 144 MET cc_start: 0.8706 (mmm) cc_final: 0.8266 (mmp) REVERT: C 205 ASP cc_start: 0.8158 (m-30) cc_final: 0.7668 (m-30) outliers start: 30 outliers final: 16 residues processed: 170 average time/residue: 0.1054 time to fit residues: 27.2679 Evaluate side-chains 159 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 269 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.164234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110325 restraints weight = 30281.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109993 restraints weight = 17709.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.110807 restraints weight = 12382.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111502 restraints weight = 10956.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111617 restraints weight = 10019.338| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13883 Z= 0.220 Angle : 0.664 13.739 19032 Z= 0.350 Chirality : 0.044 0.407 2151 Planarity : 0.004 0.071 2125 Dihedral : 20.309 59.888 2436 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.22 % Favored : 95.50 % Rotamer: Outliers : 1.92 % Allowed : 16.69 % Favored : 81.39 % 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: 1.20 (0.23), residues: 1422 helix: 1.99 (0.18), residues: 792 sheet: -0.04 (0.46), residues: 141 loop : -0.95 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 415 TYR 0.030 0.002 TYR B 287 PHE 0.038 0.002 PHE B 448 TRP 0.029 0.002 TRP C 98 HIS 0.002 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (13883) covalent geometry : angle 0.66444 / 0.35 (19032) hydrogen bonds : bond 0.04484 / 2.88 ( 819) hydrogen bonds : angle 4.37297 / 3.11 ( 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 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8507 (m-80) cc_final: 0.8173 (m-80) REVERT: A 178 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: A 251 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.7498 (mt) REVERT: A 356 LEU cc_start: 0.8824 (tp) cc_final: 0.8582 (tt) REVERT: B 35 LYS cc_start: 0.8216 (tttt) cc_final: 0.7885 (tttm) REVERT: B 82 GLN cc_start: 0.8969 (tp40) cc_final: 0.8683 (tm-30) REVERT: B 83 LYS cc_start: 0.8526 (mttt) cc_final: 0.8304 (mttp) REVERT: B 137 ASP cc_start: 0.7903 (t0) cc_final: 0.7690 (t70) REVERT: B 331 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7309 (t80) REVERT: B 347 ARG cc_start: 0.8872 (ttp80) cc_final: 0.8301 (tpm170) REVERT: B 360 ASP cc_start: 0.8815 (m-30) cc_final: 0.8574 (m-30) REVERT: B 368 LYS cc_start: 0.8924 (tttt) cc_final: 0.8443 (mmmt) REVERT: B 407 GLU cc_start: 0.9183 (tp30) cc_final: 0.8766 (tp30) REVERT: B 415 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8394 (mtp-110) REVERT: B 459 MET cc_start: 0.8360 (tpt) cc_final: 0.8064 (tpp) REVERT: C 55 PHE cc_start: 0.8211 (m-80) cc_final: 0.7956 (m-80) REVERT: C 144 MET cc_start: 0.8802 (mmm) cc_final: 0.8371 (mmp) outliers start: 26 outliers final: 19 residues processed: 162 average time/residue: 0.1096 time to fit residues: 26.7210 Evaluate side-chains 162 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU 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: 0.0980 chunk 126 optimal weight: 1.9990 chunk 142 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 0 optimal weight: 70.0000 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 8 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.164710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.112921 restraints weight = 29872.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.111956 restraints weight = 17935.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.112023 restraints weight = 13290.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112746 restraints weight = 11971.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112887 restraints weight = 11018.910| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13883 Z= 0.163 Angle : 0.642 13.828 19032 Z= 0.337 Chirality : 0.043 0.327 2151 Planarity : 0.003 0.067 2125 Dihedral : 20.304 59.886 2436 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.22 % Favored : 95.50 % Rotamer: Outliers : 1.70 % Allowed : 17.06 % 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: 1.18 (0.23), residues: 1422 helix: 2.01 (0.18), residues: 792 sheet: -0.01 (0.44), residues: 149 loop : -1.06 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 415 TYR 0.030 0.002 TYR B 45 PHE 0.036 0.002 PHE B 448 TRP 0.026 0.002 TRP C 98 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (13883) covalent geometry : angle 0.64175 / 0.34 (19032) hydrogen bonds : bond 0.04282 / 2.75 ( 819) hydrogen bonds : angle 4.34694 / 3.10 ( 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 172 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3424 (OUTLIER) cc_final: 0.3181 (t) REVERT: A 165 PHE cc_start: 0.8442 (m-80) cc_final: 0.8118 (m-80) REVERT: A 177 LEU cc_start: 0.9105 (mt) cc_final: 0.8904 (pp) REVERT: A 178 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: A 248 MET cc_start: 0.7810 (mmm) cc_final: 0.7218 (ttp) REVERT: A 251 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.7486 (mt) REVERT: A 356 LEU cc_start: 0.8830 (tp) cc_final: 0.8605 (tt) REVERT: B 35 LYS cc_start: 0.8175 (tttt) cc_final: 0.7868 (tttm) REVERT: B 83 LYS cc_start: 0.8448 (mttt) cc_final: 0.8157 (mttp) REVERT: B 137 ASP cc_start: 0.7834 (t0) cc_final: 0.7625 (t70) REVERT: B 331 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7323 (t80) REVERT: B 332 GLU cc_start: 0.8211 (tt0) cc_final: 0.7963 (tm-30) REVERT: B 347 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8295 (tpm170) REVERT: B 360 ASP cc_start: 0.8762 (m-30) cc_final: 0.8519 (m-30) REVERT: B 368 LYS cc_start: 0.8920 (tttt) cc_final: 0.8375 (mmmt) REVERT: B 395 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8441 (tp) REVERT: B 407 GLU cc_start: 0.9145 (tp30) cc_final: 0.8697 (tp30) REVERT: B 459 MET cc_start: 0.8263 (tpt) cc_final: 0.7993 (tpp) REVERT: C 55 PHE cc_start: 0.8169 (m-80) cc_final: 0.7926 (m-80) REVERT: C 144 MET cc_start: 0.8744 (mmm) cc_final: 0.8335 (mmp) outliers start: 23 outliers final: 16 residues processed: 165 average time/residue: 0.1109 time to fit residues: 27.6914 Evaluate side-chains 164 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 51 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.165043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111281 restraints weight = 29920.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112106 restraints weight = 17041.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112604 restraints weight = 11645.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113394 restraints weight = 11260.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113361 restraints weight = 9165.041| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13883 Z= 0.147 Angle : 0.634 13.990 19032 Z= 0.333 Chirality : 0.043 0.318 2151 Planarity : 0.004 0.096 2125 Dihedral : 20.298 59.879 2436 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.36 % Favored : 95.36 % Rotamer: Outliers : 1.85 % Allowed : 16.77 % Favored : 81.39 % 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: 2.05 (0.18), residues: 791 sheet: 0.26 (0.47), residues: 137 loop : -1.07 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 415 TYR 0.029 0.001 TYR B 45 PHE 0.049 0.002 PHE B 448 TRP 0.020 0.002 TRP C 98 HIS 0.004 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (13883) covalent geometry : angle 0.63399 / 0.33 (19032) hydrogen bonds : bond 0.04180 / 2.67 ( 819) hydrogen bonds : angle 4.30866 / 3.07 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.82 seconds wall clock time: 44 minutes 57.25 seconds (2697.25 seconds total)