Starting phenix.real_space_refine on Thu Aug 6 08:41:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5j_29746/08_2026/8g5j_29746_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5j_29746/08_2026/8g5j_29746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g5j_29746/08_2026/8g5j_29746_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5j_29746/08_2026/8g5j_29746_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5j_29746/08_2026/8g5j_29746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5j_29746/08_2026/8g5j_29746.map" } resolution = 2.63 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= 0.026 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 40 5.49 5 S 80 5.16 5 C 9131 2.51 5 N 2562 2.21 5 O 2731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 14544 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7369 Classifications: {'peptide': 941} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 60, 'TRANS': 880} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 5, 'TRP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3188 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 379} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3168 Classifications: {'peptide': 400} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "P" Number of atoms: 413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 419 Chain: "T" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA P 28 " occ=0.50 ... (38 atoms not shown) pdb=" C4 B DA P 28 " occ=0.50 residue: pdb=" P DG T 3 " occ=0.50 ... (20 atoms not shown) pdb=" C4 DG T 3 " occ=0.50 Time building chain proxies: 3.40, per 1000 atoms: 0.23 Number of scatterers: 14544 At special positions: 0 Unit cell: (102.424, 102.424, 145.376, 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 80 16.00 P 40 15.00 O 2731 8.00 N 2562 7.00 C 9131 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: 1.27 Conformation dependent library (CDL) restraints added in 675.7 milliseconds 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3242 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 10 sheets defined 41.1% alpha, 12.2% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.509A pdb=" N GLU A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.890A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.725A pdb=" N GLY A 303 " --> pdb=" O MET A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.063A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.501A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 removed outlier: 4.007A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 551 through 556 removed outlier: 4.041A pdb=" N THR A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.002A pdb=" N LYS A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.719A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.597A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 removed outlier: 4.166A pdb=" N ARG A 853 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 903 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.503A pdb=" N THR A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 954 removed outlier: 4.629A pdb=" N GLY A 952 " --> pdb=" O ILE A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 971 Processing helix chain 'A' and resid 973 through 984 removed outlier: 4.264A pdb=" N LYS A 981 " --> pdb=" O GLU A 977 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA A 982 " --> pdb=" O ALA A 978 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1057 through 1066 removed outlier: 4.029A pdb=" N LEU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1124 removed outlier: 3.762A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 3.624A pdb=" N ASP A1219 " --> pdb=" O GLU A1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 192 through 200 removed outlier: 3.515A pdb=" N VAL B 200 " --> pdb=" O CYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 394 through 409 removed outlier: 4.062A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.918A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.794A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.158A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.982A pdb=" N LEU C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.584A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 484 removed outlier: 4.590A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.808A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 211 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 200 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 removed outlier: 4.689A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1130 through 1133 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.294A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.157A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.263A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.865A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.71 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: 4473 1.34 - 1.46: 2636 1.46 - 1.58: 7664 1.58 - 1.70: 79 1.70 - 1.82: 126 Bond restraints: 14978 Sorted by residual: bond pdb=" C2' DG T 3 " pdb=" C1' DG T 3 " ideal model delta sigma weight residual 1.518 1.438 0.080 1.00e-02 1.00e+04 6.43e+01 bond pdb=" P DC T 4 " pdb=" OP2 DC T 4 " ideal model delta sigma weight residual 1.480 1.621 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C1' DA P 15 " pdb=" N9 DA P 15 " ideal model delta sigma weight residual 1.468 1.381 0.087 1.40e-02 5.10e+03 3.85e+01 bond pdb=" C1' DG P 16 " pdb=" N9 DG P 16 " ideal model delta sigma weight residual 1.468 1.382 0.086 1.40e-02 5.10e+03 3.78e+01 bond pdb=" P DC T 4 " pdb=" O5' DC T 4 " ideal model delta sigma weight residual 1.593 1.654 -0.061 1.00e-02 1.00e+04 3.68e+01 ... (remaining 14973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 20365 5.34 - 10.67: 97 10.67 - 16.01: 6 16.01 - 21.34: 1 21.34 - 26.68: 1 Bond angle restraints: 20470 Sorted by residual: angle pdb=" C3' DG T 3 " pdb=" O3' DG T 3 " pdb=" P DC T 4 " ideal model delta sigma weight residual 119.70 93.02 26.68 1.20e+00 6.94e-01 4.94e+02 angle pdb=" C3' DC T 2 " pdb=" O3' DC T 2 " pdb=" P DG T 3 " ideal model delta sigma weight residual 119.70 107.81 11.89 1.20e+00 6.94e-01 9.82e+01 angle pdb=" N PRO C 137 " pdb=" CA PRO C 137 " pdb=" C PRO C 137 " ideal model delta sigma weight residual 113.65 100.84 12.81 1.35e+00 5.49e-01 9.00e+01 angle pdb=" C3' DC T 4 " pdb=" O3' DC T 4 " pdb=" P DG T 5 " ideal model delta sigma weight residual 119.70 108.68 11.02 1.20e+00 6.94e-01 8.43e+01 angle pdb=" C3' DG T 3 " pdb=" C2' DG T 3 " pdb=" C1' DG T 3 " ideal model delta sigma weight residual 102.50 113.12 -10.62 1.20e+00 6.94e-01 7.84e+01 ... (remaining 20465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 8082 28.66 - 57.32: 668 57.32 - 85.97: 81 85.97 - 114.63: 0 114.63 - 143.29: 3 Dihedral angle restraints: 8834 sinusoidal: 3819 harmonic: 5015 Sorted by residual: dihedral pdb=" CD ARG A 102 " pdb=" NE ARG A 102 " pdb=" CZ ARG A 102 " pdb=" NH1 ARG A 102 " ideal model delta sinusoidal sigma weight residual 0.00 -69.84 69.84 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" CD ARG B 257 " pdb=" NE ARG B 257 " pdb=" CZ ARG B 257 " pdb=" NH1 ARG B 257 " ideal model delta sinusoidal sigma weight residual 0.00 -57.20 57.20 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CD ARG B 154 " pdb=" NE ARG B 154 " pdb=" CZ ARG B 154 " pdb=" NH1 ARG B 154 " ideal model delta sinusoidal sigma weight residual 0.00 55.71 -55.71 1 1.00e+01 1.00e-02 4.19e+01 ... (remaining 8831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 2194 0.238 - 0.476: 25 0.476 - 0.714: 8 0.714 - 0.952: 0 0.952 - 1.190: 1 Chirality restraints: 2228 Sorted by residual: chirality pdb=" P DC T 4 " pdb=" OP1 DC T 4 " pdb=" OP2 DC T 4 " pdb=" O5' DC T 4 " both_signs ideal model delta sigma weight residual True 2.34 -3.53 -1.19 2.00e-01 2.50e+01 3.54e+01 chirality pdb=" P DC T 2 " pdb=" OP1 DC T 2 " pdb=" OP2 DC T 2 " pdb=" O5' DC T 2 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DA P 10 " pdb=" OP1 DA P 10 " pdb=" OP2 DA P 10 " pdb=" O5' DA P 10 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.46e+00 ... (remaining 2225 not shown) Planarity restraints: 2497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 102 " -1.036 9.50e-02 1.11e+02 4.64e-01 1.30e+02 pdb=" NE ARG A 102 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 102 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 102 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 102 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 257 " -0.923 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG B 257 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG B 257 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 257 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 257 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 154 " -0.904 9.50e-02 1.11e+02 4.05e-01 9.96e+01 pdb=" NE ARG B 154 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG B 154 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 154 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 154 " -0.024 2.00e-02 2.50e+03 ... (remaining 2494 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 283 2.67 - 3.22: 13525 3.22 - 3.78: 23408 3.78 - 4.34: 31799 4.34 - 4.90: 51352 Nonbonded interactions: 120367 Sorted by model distance: nonbonded pdb=" OD2 ASP A 892 " pdb=" OG SER A1181 " model vdw 2.108 3.040 nonbonded pdb=" NH2 ARG B 75 " pdb=" O GLY B 81 " model vdw 2.134 3.120 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.179 3.040 nonbonded pdb=" O ASP A 491 " pdb=" NH2 ARG A 574 " model vdw 2.220 3.120 nonbonded pdb=" C2' DG T 3 " pdb=" P DC T 4 " model vdw 2.229 3.040 ... (remaining 120362 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 'B' and (resid 68 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or (r \ esid 137 and (name N or name CA or name C or name O )) or resid 138 through 219 \ or resid 229 through 283 or (resid 284 through 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 through 355 or resid 368 through 485)) selection = (chain 'C' and (resid 68 through 161 or (resid 169 through 178 and (name N or na \ me CA or name C or name O or name CB )) or resid 179 through 219 or resid 229 th \ rough 485)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.020 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 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 : 0.006 0.141 14978 Z= 0.378 Angle : 1.035 26.679 20470 Z= 0.638 Chirality : 0.078 1.190 2228 Planarity : 0.021 0.464 2497 Dihedral : 19.274 143.288 5592 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Rotamer: Outliers : 2.20 % Allowed : 25.14 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1713 helix: 1.05 (0.21), residues: 658 sheet: 0.29 (0.33), residues: 228 loop : -1.78 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 227 TYR 0.018 0.001 TYR C 291 PHE 0.039 0.001 PHE A 961 TRP 0.018 0.001 TRP A 607 HIS 0.016 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.38 (14978) covalent geometry : angle 1.03501 / 0.64 (20470) hydrogen bonds : bond 0.14209 / 9.87 ( 614) hydrogen bonds : angle 6.84950 / 4.75 ( 1723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.544 Fit side-chains REVERT: A 87 ILE cc_start: 0.2050 (OUTLIER) cc_final: 0.1459 (pp) REVERT: A 215 ILE cc_start: 0.7484 (pt) cc_final: 0.7283 (pt) REVERT: B 329 LYS cc_start: 0.7431 (ptmm) cc_final: 0.7196 (ptmt) REVERT: B 460 THR cc_start: 0.7615 (p) cc_final: 0.7225 (p) REVERT: C 397 GLN cc_start: 0.7095 (mp10) cc_final: 0.6506 (mp10) outliers start: 32 outliers final: 12 residues processed: 207 average time/residue: 0.5282 time to fit residues: 121.3855 Evaluate side-chains 172 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 144 GLN A 493 GLN A 550 GLN A 761 ASN A 811 GLN A 843 GLN A 894 GLN A 922 GLN A1059 ASN A1110 HIS A1222 GLN B 133 HIS B 272 ASN C 250 GLN C 279 GLN C 309 HIS C 330 ASN C 404 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.185080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131905 restraints weight = 31705.781| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.78 r_work: 0.3484 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14978 Z= 0.198 Angle : 0.708 12.321 20470 Z= 0.369 Chirality : 0.048 0.274 2228 Planarity : 0.006 0.063 2497 Dihedral : 16.490 143.480 2313 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.84 % Favored : 93.99 % Rotamer: Outliers : 3.85 % Allowed : 24.04 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1713 helix: 1.15 (0.20), residues: 663 sheet: 0.44 (0.33), residues: 227 loop : -1.73 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 227 TYR 0.015 0.002 TYR C 291 PHE 0.017 0.002 PHE A 610 TRP 0.015 0.001 TRP A 748 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (14978) covalent geometry : angle 0.70779 / 0.37 (20470) hydrogen bonds : bond 0.04978 / 3.35 ( 614) hydrogen bonds : angle 5.07990 / 3.43 ( 1723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.534 Fit side-chains REVERT: A 87 ILE cc_start: 0.2600 (OUTLIER) cc_final: 0.1775 (pp) REVERT: A 372 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6528 (mt-10) REVERT: A 484 TRP cc_start: 0.7937 (m-90) cc_final: 0.6897 (m-10) REVERT: B 314 MET cc_start: 0.8495 (ttm) cc_final: 0.8248 (mtp) REVERT: B 325 ARG cc_start: 0.7352 (mtm110) cc_final: 0.7086 (mtm180) REVERT: B 460 THR cc_start: 0.7944 (p) cc_final: 0.7659 (p) REVERT: C 139 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.6007 (mp) REVERT: C 355 GLN cc_start: 0.5131 (OUTLIER) cc_final: 0.4024 (pm20) outliers start: 56 outliers final: 22 residues processed: 201 average time/residue: 0.4843 time to fit residues: 108.4681 Evaluate side-chains 183 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 15 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 173 optimal weight: 40.0000 chunk 101 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 550 GLN A 803 ASN A1089 GLN A1102 GLN B 124 GLN B 187 HIS C 309 HIS C 409 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.183566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131314 restraints weight = 36448.058| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 4.27 r_work: 0.3460 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14978 Z= 0.183 Angle : 0.673 12.417 20470 Z= 0.348 Chirality : 0.046 0.257 2228 Planarity : 0.006 0.065 2497 Dihedral : 16.605 144.737 2307 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.48 % Favored : 93.35 % Rotamer: Outliers : 4.12 % Allowed : 24.45 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1713 helix: 1.15 (0.21), residues: 657 sheet: 0.44 (0.33), residues: 238 loop : -1.71 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 827 TYR 0.014 0.002 TYR C 291 PHE 0.016 0.002 PHE A 749 TRP 0.015 0.001 TRP A 748 HIS 0.007 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (14978) covalent geometry : angle 0.67296 / 0.35 (20470) hydrogen bonds : bond 0.04456 / 3.03 ( 614) hydrogen bonds : angle 4.95659 / 3.32 ( 1723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 163 time to evaluate : 0.448 Fit side-chains REVERT: A 87 ILE cc_start: 0.2432 (OUTLIER) cc_final: 0.1630 (pp) REVERT: A 108 GLN cc_start: 0.6650 (tt0) cc_final: 0.6269 (mt0) REVERT: A 183 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5880 (pm20) REVERT: A 372 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: A 484 TRP cc_start: 0.7942 (m-90) cc_final: 0.6897 (m-10) REVERT: A 603 MET cc_start: 0.4680 (OUTLIER) cc_final: 0.4421 (ppp) REVERT: A 947 LYS cc_start: 0.5790 (tmtt) cc_final: 0.5022 (ttmt) REVERT: A 1131 ILE cc_start: 0.5044 (OUTLIER) cc_final: 0.4246 (mt) REVERT: B 314 MET cc_start: 0.8424 (ttm) cc_final: 0.8194 (mtp) REVERT: B 325 ARG cc_start: 0.7383 (mtm110) cc_final: 0.7143 (mtm180) REVERT: B 421 MET cc_start: 0.6573 (pp-130) cc_final: 0.6352 (pp-130) REVERT: C 355 GLN cc_start: 0.5028 (OUTLIER) cc_final: 0.3974 (pm20) REVERT: C 400 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6860 (tm-30) outliers start: 60 outliers final: 27 residues processed: 203 average time/residue: 0.5065 time to fit residues: 114.6483 Evaluate side-chains 185 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 147 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 30 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN A 803 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.185750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132951 restraints weight = 32465.068| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.80 r_work: 0.3482 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14978 Z= 0.135 Angle : 0.629 12.423 20470 Z= 0.323 Chirality : 0.044 0.199 2228 Planarity : 0.005 0.066 2497 Dihedral : 16.541 144.641 2307 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.19 % Favored : 93.64 % Rotamer: Outliers : 3.91 % Allowed : 24.86 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1713 helix: 1.17 (0.21), residues: 669 sheet: 0.50 (0.33), residues: 238 loop : -1.76 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 75 TYR 0.010 0.001 TYR A1108 PHE 0.015 0.001 PHE B 254 TRP 0.012 0.001 TRP A 748 HIS 0.006 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (14978) covalent geometry : angle 0.62935 / 0.32 (20470) hydrogen bonds : bond 0.03973 / 2.67 ( 614) hydrogen bonds : angle 4.81493 / 3.22 ( 1723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.2383 (OUTLIER) cc_final: 0.1600 (pp) REVERT: A 94 MET cc_start: 0.5951 (tpt) cc_final: 0.5671 (tpt) REVERT: A 108 GLN cc_start: 0.6805 (tt0) cc_final: 0.6503 (mt0) REVERT: A 183 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5924 (pm20) REVERT: A 372 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: A 603 MET cc_start: 0.4673 (OUTLIER) cc_final: 0.4207 (ppp) REVERT: A 774 MET cc_start: 0.7048 (mmt) cc_final: 0.6234 (mmt) REVERT: A 985 MET cc_start: 0.5021 (mmp) cc_final: 0.4264 (mtp) REVERT: A 1131 ILE cc_start: 0.4889 (OUTLIER) cc_final: 0.4122 (mt) REVERT: B 314 MET cc_start: 0.8474 (ttm) cc_final: 0.8255 (mtp) REVERT: B 325 ARG cc_start: 0.7432 (mtm110) cc_final: 0.7202 (mtm180) REVERT: B 421 MET cc_start: 0.6570 (pp-130) cc_final: 0.6368 (pp-130) REVERT: C 134 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7612 (mmtp) REVERT: C 306 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6858 (mt) REVERT: C 355 GLN cc_start: 0.4997 (OUTLIER) cc_final: 0.3933 (pm20) REVERT: C 400 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6891 (tm-30) outliers start: 57 outliers final: 26 residues processed: 198 average time/residue: 0.5022 time to fit residues: 110.7423 Evaluate side-chains 188 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 949 PHE Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 165 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 GLN A 550 GLN A 564 GLN A 803 ASN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.184309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132063 restraints weight = 28120.431| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.55 r_work: 0.3480 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14978 Z= 0.158 Angle : 0.641 13.605 20470 Z= 0.330 Chirality : 0.045 0.198 2228 Planarity : 0.005 0.064 2497 Dihedral : 16.523 144.773 2306 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.54 % Favored : 93.29 % Rotamer: Outliers : 3.71 % Allowed : 25.48 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1713 helix: 1.21 (0.21), residues: 663 sheet: 0.55 (0.33), residues: 238 loop : -1.75 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 75 TYR 0.020 0.002 TYR C 206 PHE 0.029 0.002 PHE A 949 TRP 0.013 0.001 TRP A 748 HIS 0.007 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (14978) covalent geometry : angle 0.64069 / 0.33 (20470) hydrogen bonds : bond 0.03994 / 2.68 ( 614) hydrogen bonds : angle 4.80897 / 3.20 ( 1723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.2454 (OUTLIER) cc_final: 0.1586 (pp) REVERT: A 108 GLN cc_start: 0.6893 (tt0) cc_final: 0.6590 (mt0) REVERT: A 183 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5975 (pm20) REVERT: A 372 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6600 (mt-10) REVERT: A 484 TRP cc_start: 0.7928 (m-90) cc_final: 0.6925 (m-10) REVERT: A 603 MET cc_start: 0.4639 (OUTLIER) cc_final: 0.4367 (ppp) REVERT: A 780 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6738 (mt0) REVERT: A 1131 ILE cc_start: 0.4971 (OUTLIER) cc_final: 0.4178 (mt) REVERT: B 314 MET cc_start: 0.8486 (ttm) cc_final: 0.8283 (mtp) REVERT: B 325 ARG cc_start: 0.7473 (mtm110) cc_final: 0.7251 (mtm180) REVERT: B 421 MET cc_start: 0.6585 (pp-130) cc_final: 0.6234 (pp-130) REVERT: B 460 THR cc_start: 0.7995 (p) cc_final: 0.7729 (p) REVERT: C 134 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7710 (mmtp) REVERT: C 355 GLN cc_start: 0.5021 (OUTLIER) cc_final: 0.3914 (pm20) REVERT: C 400 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6896 (tm-30) outliers start: 54 outliers final: 26 residues processed: 197 average time/residue: 0.4667 time to fit residues: 103.1409 Evaluate side-chains 187 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN A 803 ASN A 828 HIS A 911 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.183452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130084 restraints weight = 35964.615| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.95 r_work: 0.3449 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14978 Z= 0.162 Angle : 0.644 12.106 20470 Z= 0.330 Chirality : 0.045 0.202 2228 Planarity : 0.005 0.067 2497 Dihedral : 16.533 144.753 2305 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.65 % Favored : 93.17 % Rotamer: Outliers : 3.91 % Allowed : 25.27 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1713 helix: 1.20 (0.21), residues: 657 sheet: 0.53 (0.33), residues: 238 loop : -1.65 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 75 TYR 0.016 0.002 TYR C 206 PHE 0.026 0.002 PHE A 961 TRP 0.015 0.001 TRP A 748 HIS 0.006 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (14978) covalent geometry : angle 0.64384 / 0.33 (20470) hydrogen bonds : bond 0.03939 / 2.63 ( 614) hydrogen bonds : angle 4.81866 / 3.21 ( 1723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 0.543 Fit side-chains REVERT: A 108 GLN cc_start: 0.6900 (tt0) cc_final: 0.6190 (mt0) REVERT: A 120 LEU cc_start: 0.8886 (mp) cc_final: 0.8668 (tp) REVERT: A 183 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5955 (pm20) REVERT: A 372 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: A 484 TRP cc_start: 0.7935 (m-90) cc_final: 0.6937 (m-10) REVERT: A 603 MET cc_start: 0.4641 (OUTLIER) cc_final: 0.4378 (ppp) REVERT: A 780 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: A 910 MET cc_start: 0.7930 (mpp) cc_final: 0.7689 (mpt) REVERT: A 1131 ILE cc_start: 0.5070 (OUTLIER) cc_final: 0.4258 (mt) REVERT: B 394 GLU cc_start: 0.7942 (tp30) cc_final: 0.7703 (tp30) REVERT: B 421 MET cc_start: 0.6629 (pp-130) cc_final: 0.6348 (pp-130) REVERT: B 460 THR cc_start: 0.8020 (p) cc_final: 0.7766 (p) REVERT: C 355 GLN cc_start: 0.5050 (OUTLIER) cc_final: 0.3939 (pm20) REVERT: C 400 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6934 (tm-30) outliers start: 57 outliers final: 29 residues processed: 205 average time/residue: 0.5103 time to fit residues: 116.8180 Evaluate side-chains 189 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 65 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN A 803 ASN A1214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.184205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130630 restraints weight = 37966.954| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 4.05 r_work: 0.3450 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14978 Z= 0.145 Angle : 0.631 11.179 20470 Z= 0.324 Chirality : 0.044 0.205 2228 Planarity : 0.005 0.065 2497 Dihedral : 16.517 144.838 2303 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.48 % Favored : 93.35 % Rotamer: Outliers : 3.78 % Allowed : 25.62 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1713 helix: 1.21 (0.21), residues: 663 sheet: 0.52 (0.33), residues: 238 loop : -1.73 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 75 TYR 0.012 0.001 TYR C 206 PHE 0.026 0.001 PHE A 961 TRP 0.013 0.001 TRP A 748 HIS 0.006 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14978) covalent geometry : angle 0.63097 / 0.32 (20470) hydrogen bonds : bond 0.03775 / 2.51 ( 614) hydrogen bonds : angle 4.78537 / 3.18 ( 1723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.6894 (tt0) cc_final: 0.6176 (mt0) REVERT: A 183 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5930 (pm20) REVERT: A 372 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6571 (mt-10) REVERT: A 603 MET cc_start: 0.4617 (OUTLIER) cc_final: 0.4154 (ppp) REVERT: A 780 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.7027 (pt0) REVERT: A 947 LYS cc_start: 0.5629 (tptt) cc_final: 0.4845 (ttmt) REVERT: A 1121 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: A 1131 ILE cc_start: 0.4988 (OUTLIER) cc_final: 0.4185 (mt) REVERT: B 394 GLU cc_start: 0.7973 (tp30) cc_final: 0.7510 (tp30) REVERT: B 421 MET cc_start: 0.6624 (pp-130) cc_final: 0.6389 (pp-130) REVERT: B 453 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7272 (pp) REVERT: C 355 GLN cc_start: 0.5010 (OUTLIER) cc_final: 0.3928 (pm20) REVERT: C 400 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6910 (tm-30) outliers start: 55 outliers final: 30 residues processed: 202 average time/residue: 0.4369 time to fit residues: 99.1199 Evaluate side-chains 191 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 97 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 104 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 11 optimal weight: 0.0000 chunk 141 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 155 optimal weight: 0.2980 chunk 119 optimal weight: 0.6980 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.187383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134267 restraints weight = 37865.710| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 4.48 r_work: 0.3489 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14978 Z= 0.114 Angle : 0.603 14.176 20470 Z= 0.310 Chirality : 0.043 0.206 2228 Planarity : 0.005 0.067 2497 Dihedral : 16.456 144.879 2303 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.07 % Favored : 93.75 % Rotamer: Outliers : 3.09 % Allowed : 26.44 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1713 helix: 1.28 (0.21), residues: 669 sheet: 0.54 (0.33), residues: 238 loop : -1.68 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 827 TYR 0.011 0.001 TYR C 206 PHE 0.028 0.001 PHE A 961 TRP 0.019 0.001 TRP A 918 HIS 0.006 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (14978) covalent geometry : angle 0.60335 / 0.31 (20470) hydrogen bonds : bond 0.03437 / 2.26 ( 614) hydrogen bonds : angle 4.71249 / 3.13 ( 1723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.6914 (tt0) cc_final: 0.6265 (mt0) REVERT: A 183 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5892 (pm20) REVERT: A 372 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6530 (mt-10) REVERT: A 603 MET cc_start: 0.4683 (OUTLIER) cc_final: 0.4189 (ppp) REVERT: A 890 ASP cc_start: 0.7988 (p0) cc_final: 0.7635 (p0) REVERT: A 910 MET cc_start: 0.7857 (mpp) cc_final: 0.7591 (mpt) REVERT: A 947 LYS cc_start: 0.5783 (tptt) cc_final: 0.5047 (ttmt) REVERT: A 1121 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: A 1131 ILE cc_start: 0.4890 (OUTLIER) cc_final: 0.4106 (mt) REVERT: B 352 ASP cc_start: 0.7547 (t0) cc_final: 0.7336 (t70) REVERT: B 394 GLU cc_start: 0.8017 (tp30) cc_final: 0.7499 (tp30) REVERT: B 421 MET cc_start: 0.6698 (pp-130) cc_final: 0.6463 (pp-130) REVERT: C 397 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6546 (mp10) REVERT: C 400 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6864 (tm-30) outliers start: 45 outliers final: 20 residues processed: 195 average time/residue: 0.4725 time to fit residues: 102.3502 Evaluate side-chains 181 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 74 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.183099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129892 restraints weight = 33548.277| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.84 r_work: 0.3451 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14978 Z= 0.181 Angle : 0.660 14.803 20470 Z= 0.337 Chirality : 0.045 0.207 2228 Planarity : 0.005 0.065 2497 Dihedral : 16.499 144.825 2303 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.01 % Favored : 92.82 % Rotamer: Outliers : 2.95 % Allowed : 27.13 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.21), residues: 1713 helix: 1.26 (0.21), residues: 657 sheet: 0.54 (0.33), residues: 238 loop : -1.64 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 75 TYR 0.013 0.002 TYR A 434 PHE 0.029 0.002 PHE A 961 TRP 0.017 0.001 TRP A 918 HIS 0.006 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (14978) covalent geometry : angle 0.65962 / 0.34 (20470) hydrogen bonds : bond 0.03888 / 2.58 ( 614) hydrogen bonds : angle 4.80747 / 3.19 ( 1723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.541 Fit side-chains REVERT: A 108 GLN cc_start: 0.6924 (tt0) cc_final: 0.6200 (mt0) REVERT: A 183 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5936 (pm20) REVERT: A 227 ARG cc_start: 0.7368 (ptp-110) cc_final: 0.7033 (mtm110) REVERT: A 372 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6520 (mt-10) REVERT: A 603 MET cc_start: 0.4556 (OUTLIER) cc_final: 0.4195 (ppp) REVERT: A 947 LYS cc_start: 0.5825 (tptt) cc_final: 0.5077 (ttmt) REVERT: A 1121 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: B 394 GLU cc_start: 0.8092 (tp30) cc_final: 0.7602 (tp30) REVERT: B 460 THR cc_start: 0.8013 (p) cc_final: 0.7732 (p) REVERT: C 400 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6932 (tm-30) outliers start: 43 outliers final: 26 residues processed: 186 average time/residue: 0.4955 time to fit residues: 103.1980 Evaluate side-chains 182 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 43 optimal weight: 0.0270 chunk 106 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.185905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132958 restraints weight = 35050.616| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.90 r_work: 0.3486 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14978 Z= 0.123 Angle : 0.622 14.798 20470 Z= 0.319 Chirality : 0.043 0.295 2228 Planarity : 0.005 0.066 2497 Dihedral : 16.453 144.918 2303 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.30 % Favored : 93.52 % Rotamer: Outliers : 2.47 % Allowed : 27.61 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1713 helix: 1.33 (0.21), residues: 663 sheet: 0.55 (0.33), residues: 238 loop : -1.69 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 827 TYR 0.010 0.001 TYR A 434 PHE 0.027 0.001 PHE A 961 TRP 0.019 0.001 TRP A 918 HIS 0.006 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14978) covalent geometry : angle 0.62229 / 0.32 (20470) hydrogen bonds : bond 0.03527 / 2.33 ( 614) hydrogen bonds : angle 4.74187 / 3.15 ( 1723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.6933 (tt0) cc_final: 0.6281 (mt0) REVERT: A 183 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5931 (pm20) REVERT: A 227 ARG cc_start: 0.7314 (ptp-110) cc_final: 0.6970 (mtm110) REVERT: A 372 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: A 603 MET cc_start: 0.4574 (OUTLIER) cc_final: 0.4100 (ppp) REVERT: A 890 ASP cc_start: 0.7986 (p0) cc_final: 0.7637 (p0) REVERT: A 947 LYS cc_start: 0.5818 (tptt) cc_final: 0.5067 (ttmt) REVERT: A 1121 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: A 1131 ILE cc_start: 0.4872 (OUTLIER) cc_final: 0.4076 (mt) REVERT: B 394 GLU cc_start: 0.8038 (tp30) cc_final: 0.7556 (tp30) REVERT: B 460 THR cc_start: 0.7977 (p) cc_final: 0.7707 (p) REVERT: C 397 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6487 (mp10) REVERT: C 400 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6890 (tm-30) outliers start: 36 outliers final: 23 residues processed: 184 average time/residue: 0.4716 time to fit residues: 96.2554 Evaluate side-chains 188 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 145 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 149 optimal weight: 0.9980 chunk 173 optimal weight: 40.0000 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 0.0020 chunk 62 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.185691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133211 restraints weight = 32026.553| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.74 r_work: 0.3494 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14978 Z= 0.128 Angle : 0.637 14.454 20470 Z= 0.322 Chirality : 0.043 0.233 2228 Planarity : 0.005 0.065 2497 Dihedral : 16.402 144.979 2301 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.42 % Favored : 93.40 % Rotamer: Outliers : 2.34 % Allowed : 27.47 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1713 helix: 1.37 (0.21), residues: 657 sheet: 0.60 (0.33), residues: 238 loop : -1.59 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 126 TYR 0.010 0.001 TYR A 434 PHE 0.029 0.001 PHE A 961 TRP 0.018 0.001 TRP A 918 HIS 0.006 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14978) covalent geometry : angle 0.63704 / 0.32 (20470) hydrogen bonds : bond 0.03515 / 2.32 ( 614) hydrogen bonds : angle 4.72326 / 3.13 ( 1723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5577.18 seconds wall clock time: 95 minutes 28.08 seconds (5728.08 seconds total)