Starting phenix.real_space_refine on Tue Mar 3 21:46:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gjc_51387/03_2026/9gjc_51387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gjc_51387/03_2026/9gjc_51387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gjc_51387/03_2026/9gjc_51387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gjc_51387/03_2026/9gjc_51387.map" model { file = "/net/cci-nas-00/data/ceres_data/9gjc_51387/03_2026/9gjc_51387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gjc_51387/03_2026/9gjc_51387.cif" } resolution = 3.9 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= 0.003 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 5378 2.51 5 N 1454 2.21 5 O 1757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8677 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 6243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6243 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 20, 'TRANS': 776} Chain breaks: 1 Chain: "L" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2270 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 8677 At special positions: 0 Unit cell: (102.336, 113.984, 113.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 1757 8.00 N 1454 7.00 C 5378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 395 " - pdb=" SG CYS H 404 " distance=2.03 Simple disulfide: pdb=" SG CYS H 400 " - pdb=" SG CYS H 410 " distance=2.03 Simple disulfide: pdb=" SG CYS H 412 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 415 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 420 " - pdb=" SG CYS H 456 " distance=2.03 Simple disulfide: pdb=" SG CYS H 446 " - pdb=" SG CYS H 462 " distance=2.04 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS H 471 " - pdb=" SG CYS H 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 477 " - pdb=" SG CYS H 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 498 " - pdb=" SG CYS H 522 " distance=2.03 Simple disulfide: pdb=" SG CYS H 510 " - pdb=" SG CYS H 544 " distance=2.03 Simple disulfide: pdb=" SG CYS H 532 " - pdb=" SG CYS H 550 " distance=2.03 Simple disulfide: pdb=" SG CYS H 539 " - pdb=" SG CYS H 573 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 580 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 603 " distance=2.03 Simple disulfide: pdb=" SG CYS H 586 " - pdb=" SG CYS H 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 592 " - pdb=" SG CYS H 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 601 " - pdb=" SG CYS H 613 " distance=2.04 Simple disulfide: pdb=" SG CYS H 622 " - pdb=" SG CYS H 639 " distance=2.03 Simple disulfide: pdb=" SG CYS H 644 " - pdb=" SG CYS H 658 " distance=2.03 Simple disulfide: pdb=" SG CYS H 653 " - pdb=" SG CYS H 697 " distance=2.03 Simple disulfide: pdb=" SG CYS H 672 " - pdb=" SG CYS H 702 " distance=2.03 Simple disulfide: pdb=" SG CYS H 689 " - pdb=" SG CYS H 718 " distance=2.03 Simple disulfide: pdb=" SG CYS H 715 " - pdb=" SG CYS H 746 " distance=2.03 Simple disulfide: pdb=" SG CYS H 732 " - pdb=" SG CYS H 756 " distance=2.03 Simple disulfide: pdb=" SG CYS H 739 " - pdb=" SG CYS H 775 " distance=2.03 Simple disulfide: pdb=" SG CYS H 772 " - pdb=" SG CYS H 798 " distance=2.03 Simple disulfide: pdb=" SG CYS H 780 " - pdb=" SG CYS H 811 " distance=2.03 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 274 " distance=2.03 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 Links applied ALPHA1-2 " MAN B 4 " - " MAN B 5 " " MAN B 5 " - " MAN B 6 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN H 337 " " NAG B 1 " - " ASN H 390 " " NAG H 901 " - " ASN H 468 " " NAG H 902 " - " ASN H 198 " " NAG H 903 " - " ASN H 659 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 234.9 milliseconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 24 sheets defined 13.9% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.539A pdb=" N ASP H 93 " --> pdb=" O LYS H 90 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE H 94 " --> pdb=" O VAL H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.705A pdb=" N ILE H 129 " --> pdb=" O GLU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 200 removed outlier: 3.943A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN H 198 " --> pdb=" O GLN H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 235 removed outlier: 4.317A pdb=" N LYS H 229 " --> pdb=" O SER H 225 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER H 230 " --> pdb=" O THR H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 241 removed outlier: 3.513A pdb=" N GLN H 240 " --> pdb=" O LEU H 237 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU H 241 " --> pdb=" O LEU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 273 removed outlier: 3.645A pdb=" N VAL H 273 " --> pdb=" O TYR H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 299 removed outlier: 4.037A pdb=" N ASP H 299 " --> pdb=" O THR H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 333 removed outlier: 3.534A pdb=" N GLU H 332 " --> pdb=" O ASN H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 361 removed outlier: 3.955A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG H 359 " --> pdb=" O ARG H 355 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU H 360 " --> pdb=" O SER H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 389 Processing helix chain 'H' and resid 560 through 564 Processing helix chain 'H' and resid 604 through 608 Processing helix chain 'H' and resid 684 through 688 Processing helix chain 'H' and resid 767 through 774 removed outlier: 3.997A pdb=" N GLU H 774 " --> pdb=" O ASP H 770 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 99 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 278 through 281 Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108 removed outlier: 4.726A pdb=" N GLY H 36 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP H 29 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 104 through 108 Processing sheet with id=AA3, first strand: chain 'H' and resid 257 through 262 removed outlier: 6.796A pdb=" N THR H 214 " --> pdb=" O LYS H 245 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL H 247 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU H 216 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU H 249 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE H 218 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR H 251 " --> pdb=" O ILE H 218 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE H 220 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS H 215 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE H 316 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA H 217 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU H 318 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE H 219 " --> pdb=" O LEU H 318 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N HIS H 368 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR H 342 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE H 370 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL H 344 " --> pdb=" O PHE H 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 423 through 425 Processing sheet with id=AA5, first strand: chain 'H' and resid 452 through 456 removed outlier: 6.700A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AA7, first strand: chain 'H' and resid 511 through 513 removed outlier: 6.426A pdb=" N SER H 512 " --> pdb=" O ASP H 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 540 through 544 Processing sheet with id=AA9, first strand: chain 'H' and resid 569 through 572 removed outlier: 3.716A pdb=" N LYS H 572 " --> pdb=" O GLU H 581 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 581 " --> pdb=" O LYS H 572 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 601 through 602 removed outlier: 4.381A pdb=" N LYS H 602 " --> pdb=" O GLN H 612 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN H 612 " --> pdb=" O LYS H 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 628 through 630 Processing sheet with id=AB3, first strand: chain 'H' and resid 650 through 651 Processing sheet with id=AB4, first strand: chain 'H' and resid 693 through 698 Processing sheet with id=AB5, first strand: chain 'H' and resid 717 through 720 Processing sheet with id=AB6, first strand: chain 'H' and resid 745 through 749 removed outlier: 3.574A pdb=" N GLY H 749 " --> pdb=" O SER H 753 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 787 through 791 Processing sheet with id=AB8, first strand: chain 'H' and resid 809 through 812 Processing sheet with id=AB9, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.353A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AC2, first strand: chain 'L' and resid 103 through 107 removed outlier: 6.449A pdb=" N ILE L 126 " --> pdb=" O ILE L 269 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE L 269 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 140 through 143 removed outlier: 3.618A pdb=" N THR L 149 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 156 through 160 Processing sheet with id=AC5, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AC6, first strand: chain 'L' and resid 207 through 212 227 hydrogen bonds defined for protein. 585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.83 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: 2797 1.34 - 1.46: 2085 1.46 - 1.58: 3861 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 8849 Sorted by residual: bond pdb=" N THR H 470 " pdb=" CA THR H 470 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.41e+00 bond pdb=" N ASP H 469 " pdb=" CA ASP H 469 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.93e+00 bond pdb=" N ASN H 468 " pdb=" CA ASN H 468 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.14e-02 7.69e+03 4.89e+00 bond pdb=" N TYR H 467 " pdb=" CA TYR H 467 " ideal model delta sigma weight residual 1.454 1.473 -0.019 1.21e-02 6.83e+03 2.43e+00 bond pdb=" C ASN H 468 " pdb=" O ASN H 468 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.07e-02 8.73e+03 1.41e+00 ... (remaining 8844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 11831 2.27 - 4.53: 120 4.53 - 6.80: 13 6.80 - 9.06: 2 9.06 - 11.33: 2 Bond angle restraints: 11968 Sorted by residual: angle pdb=" C ASN H 750 " pdb=" CA ASN H 750 " pdb=" CB ASN H 750 " ideal model delta sigma weight residual 117.23 110.78 6.45 1.36e+00 5.41e-01 2.25e+01 angle pdb=" CB MET H 478 " pdb=" CG MET H 478 " pdb=" SD MET H 478 " ideal model delta sigma weight residual 112.70 124.03 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CA ASN H 750 " pdb=" C ASN H 750 " pdb=" N ASP H 751 " ideal model delta sigma weight residual 119.98 117.00 2.98 8.50e-01 1.38e+00 1.23e+01 angle pdb=" CA ASP H 469 " pdb=" C ASP H 469 " pdb=" O ASP H 469 " ideal model delta sigma weight residual 121.56 117.98 3.58 1.09e+00 8.42e-01 1.08e+01 angle pdb=" C ASP H 458 " pdb=" N LEU H 459 " pdb=" CA LEU H 459 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.46e+00 ... (remaining 11963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4793 17.82 - 35.64: 598 35.64 - 53.46: 182 53.46 - 71.28: 40 71.28 - 89.10: 15 Dihedral angle restraints: 5628 sinusoidal: 2459 harmonic: 3169 Sorted by residual: dihedral pdb=" CB CYS H 446 " pdb=" SG CYS H 446 " pdb=" SG CYS H 462 " pdb=" CB CYS H 462 " ideal model delta sinusoidal sigma weight residual 93.00 -177.90 -89.10 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS H 557 " pdb=" SG CYS H 557 " pdb=" SG CYS H 580 " pdb=" CB CYS H 580 " ideal model delta sinusoidal sigma weight residual -86.00 -160.06 74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS H 532 " pdb=" SG CYS H 532 " pdb=" SG CYS H 550 " pdb=" CB CYS H 550 " ideal model delta sinusoidal sigma weight residual -86.00 -16.56 -69.44 1 1.00e+01 1.00e-02 6.23e+01 ... (remaining 5625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 966 0.043 - 0.085: 288 0.085 - 0.128: 75 0.128 - 0.171: 7 0.171 - 0.213: 3 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CA TYR H 467 " pdb=" N TYR H 467 " pdb=" C TYR H 467 " pdb=" CB TYR H 467 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 NAG H 901 " pdb=" ND2 ASN H 468 " pdb=" C2 NAG H 901 " pdb=" O5 NAG H 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 390 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 1336 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 223 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO L 224 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 224 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 224 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 385 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C LYS H 385 " -0.027 2.00e-02 2.50e+03 pdb=" O LYS H 385 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY H 386 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 350 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO H 351 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 351 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 351 " -0.020 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 412 2.72 - 3.27: 8482 3.27 - 3.81: 13365 3.81 - 4.36: 16004 4.36 - 4.90: 27389 Nonbonded interactions: 65652 Sorted by model distance: nonbonded pdb=" O TYR H 195 " pdb=" OG1 THR H 199 " model vdw 2.177 3.040 nonbonded pdb=" NE2 GLN H 472 " pdb=" O PRO H 473 " model vdw 2.239 3.120 nonbonded pdb=" OD2 ASP L 159 " pdb=" NE2 GLN L 188 " model vdw 2.260 3.120 nonbonded pdb=" O ARG L 68 " pdb=" OH TYR L 151 " model vdw 2.267 3.040 nonbonded pdb=" O ASP L 181 " pdb=" NH2 ARG L 186 " model vdw 2.269 3.120 ... (remaining 65647 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8896 Z= 0.131 Angle : 0.601 11.325 12075 Z= 0.319 Chirality : 0.043 0.213 1339 Planarity : 0.003 0.049 1531 Dihedral : 16.936 88.500 3494 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.83 % Allowed : 24.95 % Favored : 74.22 % 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: -0.60 (0.25), residues: 1066 helix: -1.16 (0.51), residues: 110 sheet: 0.01 (0.32), residues: 254 loop : -0.38 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 549 TYR 0.019 0.001 TYR H 717 PHE 0.016 0.001 PHE H 258 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8849) covalent geometry : angle 0.58900 (11968) SS BOND : bond 0.00245 ( 34) SS BOND : angle 1.23142 ( 68) hydrogen bonds : bond 0.15625 ( 201) hydrogen bonds : angle 6.57034 ( 585) link_ALPHA1-2 : bond 0.00338 ( 2) link_ALPHA1-2 : angle 1.43470 ( 6) link_ALPHA1-3 : bond 0.00597 ( 1) link_ALPHA1-3 : angle 1.37150 ( 3) link_ALPHA1-6 : bond 0.00635 ( 1) link_ALPHA1-6 : angle 1.19359 ( 3) link_BETA1-4 : bond 0.00438 ( 4) link_BETA1-4 : angle 1.87539 ( 12) link_NAG-ASN : bond 0.00721 ( 5) link_NAG-ASN : angle 1.78815 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 118 average time/residue: 0.0830 time to fit residues: 14.0947 Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 390 ASN Chi-restraints excluded: chain H residue 567 SER Chi-restraints excluded: chain L residue 91 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0670 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 61 optimal weight: 20.0000 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 59 GLN H 234 ASN H 548 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.192476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156629 restraints weight = 10577.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.153680 restraints weight = 13956.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155661 restraints weight = 13193.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.156217 restraints weight = 9391.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.156723 restraints weight = 9073.993| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8896 Z= 0.094 Angle : 0.544 7.999 12075 Z= 0.277 Chirality : 0.043 0.213 1339 Planarity : 0.003 0.046 1531 Dihedral : 8.445 71.376 1447 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.38 % Allowed : 23.08 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.25), residues: 1066 helix: -0.90 (0.47), residues: 123 sheet: -0.06 (0.32), residues: 252 loop : -0.33 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 549 TYR 0.010 0.001 TYR H 467 PHE 0.016 0.001 PHE H 258 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.000 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8849) covalent geometry : angle 0.52651 (11968) SS BOND : bond 0.00249 ( 34) SS BOND : angle 1.22858 ( 68) hydrogen bonds : bond 0.03349 ( 201) hydrogen bonds : angle 5.23076 ( 585) link_ALPHA1-2 : bond 0.00403 ( 2) link_ALPHA1-2 : angle 1.52442 ( 6) link_ALPHA1-3 : bond 0.01004 ( 1) link_ALPHA1-3 : angle 1.26376 ( 3) link_ALPHA1-6 : bond 0.00657 ( 1) link_ALPHA1-6 : angle 1.37679 ( 3) link_BETA1-4 : bond 0.00431 ( 4) link_BETA1-4 : angle 2.46942 ( 12) link_NAG-ASN : bond 0.00551 ( 5) link_NAG-ASN : angle 2.01483 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 151 TYR cc_start: 0.7723 (t80) cc_final: 0.7515 (t80) REVERT: L 188 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8082 (mp10) outliers start: 23 outliers final: 9 residues processed: 139 average time/residue: 0.0802 time to fit residues: 16.2552 Evaluate side-chains 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 418 ASN Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 607 THR Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain L residue 188 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.178685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143304 restraints weight = 10934.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141046 restraints weight = 16706.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142168 restraints weight = 18315.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144130 restraints weight = 11765.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144292 restraints weight = 9512.568| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8896 Z= 0.206 Angle : 0.604 6.888 12075 Z= 0.311 Chirality : 0.046 0.265 1339 Planarity : 0.004 0.051 1531 Dihedral : 7.663 63.811 1440 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.90 % Allowed : 23.19 % Favored : 73.91 % 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: -0.70 (0.25), residues: 1066 helix: -0.69 (0.50), residues: 117 sheet: -0.06 (0.32), residues: 263 loop : -0.56 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 102 TYR 0.018 0.002 TYR L 226 PHE 0.018 0.002 PHE H 258 TRP 0.014 0.002 TRP H 435 HIS 0.004 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 8849) covalent geometry : angle 0.58626 (11968) SS BOND : bond 0.00407 ( 34) SS BOND : angle 1.27174 ( 68) hydrogen bonds : bond 0.03534 ( 201) hydrogen bonds : angle 5.26270 ( 585) link_ALPHA1-2 : bond 0.00375 ( 2) link_ALPHA1-2 : angle 1.50245 ( 6) link_ALPHA1-3 : bond 0.01017 ( 1) link_ALPHA1-3 : angle 1.56551 ( 3) link_ALPHA1-6 : bond 0.00568 ( 1) link_ALPHA1-6 : angle 1.48729 ( 3) link_BETA1-4 : bond 0.00464 ( 4) link_BETA1-4 : angle 2.73272 ( 12) link_NAG-ASN : bond 0.00621 ( 5) link_NAG-ASN : angle 2.01961 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 327 PHE cc_start: 0.8021 (t80) cc_final: 0.7687 (t80) REVERT: H 531 MET cc_start: 0.7001 (mmm) cc_final: 0.6713 (tpt) REVERT: H 720 MET cc_start: 0.8072 (tpp) cc_final: 0.7423 (tpp) REVERT: L 151 TYR cc_start: 0.7991 (t80) cc_final: 0.7689 (t80) REVERT: L 188 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7979 (mp10) outliers start: 28 outliers final: 15 residues processed: 135 average time/residue: 0.0813 time to fit residues: 15.7346 Evaluate side-chains 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 567 SER Chi-restraints excluded: chain H residue 607 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 211 THR Chi-restraints excluded: chain L residue 240 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.180675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.152869 restraints weight = 10951.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151329 restraints weight = 18232.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152606 restraints weight = 16726.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152028 restraints weight = 11605.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152788 restraints weight = 11445.989| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8896 Z= 0.107 Angle : 0.544 7.925 12075 Z= 0.279 Chirality : 0.043 0.255 1339 Planarity : 0.003 0.048 1531 Dihedral : 7.126 56.761 1440 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.48 % Allowed : 24.84 % Favored : 72.67 % 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: -0.62 (0.25), residues: 1066 helix: -0.59 (0.51), residues: 117 sheet: -0.11 (0.31), residues: 262 loop : -0.45 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 549 TYR 0.015 0.001 TYR H 717 PHE 0.016 0.001 PHE H 258 TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8849) covalent geometry : angle 0.52724 (11968) SS BOND : bond 0.00418 ( 34) SS BOND : angle 1.25420 ( 68) hydrogen bonds : bond 0.02915 ( 201) hydrogen bonds : angle 5.22424 ( 585) link_ALPHA1-2 : bond 0.00401 ( 2) link_ALPHA1-2 : angle 1.48046 ( 6) link_ALPHA1-3 : bond 0.01004 ( 1) link_ALPHA1-3 : angle 1.44403 ( 3) link_ALPHA1-6 : bond 0.00789 ( 1) link_ALPHA1-6 : angle 1.40867 ( 3) link_BETA1-4 : bond 0.00539 ( 4) link_BETA1-4 : angle 2.38227 ( 12) link_NAG-ASN : bond 0.00574 ( 5) link_NAG-ASN : angle 1.80802 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 327 PHE cc_start: 0.8016 (t80) cc_final: 0.7539 (t80) REVERT: H 537 ASN cc_start: 0.7438 (p0) cc_final: 0.6445 (p0) REVERT: H 720 MET cc_start: 0.7956 (tpp) cc_final: 0.7592 (tpp) REVERT: L 151 TYR cc_start: 0.8005 (t80) cc_final: 0.7595 (t80) outliers start: 24 outliers final: 15 residues processed: 130 average time/residue: 0.0858 time to fit residues: 16.0532 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 315 MET Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 418 ASN Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 607 THR Chi-restraints excluded: chain H residue 653 CYS Chi-restraints excluded: chain L residue 211 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.196561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138009 restraints weight = 11871.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141822 restraints weight = 8284.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144106 restraints weight = 6530.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145914 restraints weight = 5639.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146558 restraints weight = 5123.585| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8896 Z= 0.212 Angle : 0.627 7.809 12075 Z= 0.322 Chirality : 0.046 0.259 1339 Planarity : 0.004 0.051 1531 Dihedral : 7.265 57.959 1440 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.45 % Allowed : 22.15 % Favored : 73.40 % 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: -0.84 (0.25), residues: 1066 helix: -0.60 (0.51), residues: 116 sheet: -0.38 (0.30), residues: 273 loop : -0.58 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 549 TYR 0.017 0.002 TYR L 226 PHE 0.017 0.002 PHE H 258 TRP 0.015 0.002 TRP H 66 HIS 0.004 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 8849) covalent geometry : angle 0.60632 (11968) SS BOND : bond 0.00351 ( 34) SS BOND : angle 1.64763 ( 68) hydrogen bonds : bond 0.03373 ( 201) hydrogen bonds : angle 5.30770 ( 585) link_ALPHA1-2 : bond 0.00286 ( 2) link_ALPHA1-2 : angle 1.46315 ( 6) link_ALPHA1-3 : bond 0.01113 ( 1) link_ALPHA1-3 : angle 1.47069 ( 3) link_ALPHA1-6 : bond 0.00534 ( 1) link_ALPHA1-6 : angle 1.53532 ( 3) link_BETA1-4 : bond 0.00551 ( 4) link_BETA1-4 : angle 2.55840 ( 12) link_NAG-ASN : bond 0.00601 ( 5) link_NAG-ASN : angle 1.97643 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 327 PHE cc_start: 0.8271 (t80) cc_final: 0.7656 (t80) REVERT: H 531 MET cc_start: 0.7609 (tpt) cc_final: 0.7287 (tpt) REVERT: H 565 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: H 720 MET cc_start: 0.8296 (tpp) cc_final: 0.8026 (tpp) REVERT: H 741 ASN cc_start: 0.8206 (t0) cc_final: 0.7720 (p0) REVERT: L 51 GLN cc_start: 0.8439 (pp30) cc_final: 0.7717 (pp30) REVERT: L 151 TYR cc_start: 0.8193 (t80) cc_final: 0.7796 (t80) outliers start: 43 outliers final: 29 residues processed: 141 average time/residue: 0.0805 time to fit residues: 16.4824 Evaluate side-chains 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 446 CYS Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 532 CYS Chi-restraints excluded: chain H residue 565 GLU Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 607 THR Chi-restraints excluded: chain H residue 653 CYS Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 201 TYR Chi-restraints excluded: chain L residue 211 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.207131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161106 restraints weight = 11934.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.160726 restraints weight = 12198.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162575 restraints weight = 11602.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164240 restraints weight = 6891.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165502 restraints weight = 5849.210| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8896 Z= 0.126 Angle : 0.560 9.632 12075 Z= 0.285 Chirality : 0.044 0.258 1339 Planarity : 0.003 0.050 1531 Dihedral : 6.703 52.975 1440 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.42 % Allowed : 23.81 % Favored : 72.77 % 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: -0.77 (0.25), residues: 1066 helix: -0.55 (0.51), residues: 116 sheet: -0.32 (0.31), residues: 271 loop : -0.53 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 549 TYR 0.011 0.001 TYR H 367 PHE 0.016 0.001 PHE H 258 TRP 0.014 0.001 TRP H 66 HIS 0.002 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8849) covalent geometry : angle 0.54480 (11968) SS BOND : bond 0.00279 ( 34) SS BOND : angle 1.13617 ( 68) hydrogen bonds : bond 0.02878 ( 201) hydrogen bonds : angle 5.13604 ( 585) link_ALPHA1-2 : bond 0.00336 ( 2) link_ALPHA1-2 : angle 1.42508 ( 6) link_ALPHA1-3 : bond 0.00936 ( 1) link_ALPHA1-3 : angle 1.54744 ( 3) link_ALPHA1-6 : bond 0.00592 ( 1) link_ALPHA1-6 : angle 1.57889 ( 3) link_BETA1-4 : bond 0.00541 ( 4) link_BETA1-4 : angle 2.35848 ( 12) link_NAG-ASN : bond 0.00560 ( 5) link_NAG-ASN : angle 1.80268 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 327 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7600 (t80) REVERT: H 443 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8579 (ptmm) REVERT: H 531 MET cc_start: 0.7524 (tpt) cc_final: 0.7308 (tpt) REVERT: H 537 ASN cc_start: 0.7945 (p0) cc_final: 0.7177 (p0) REVERT: H 720 MET cc_start: 0.8243 (tpp) cc_final: 0.8010 (tpp) REVERT: L 151 TYR cc_start: 0.8096 (t80) cc_final: 0.7615 (t80) outliers start: 33 outliers final: 21 residues processed: 125 average time/residue: 0.0842 time to fit residues: 15.3799 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 443 LYS Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 515 CYS Chi-restraints excluded: chain H residue 532 CYS Chi-restraints excluded: chain H residue 607 THR Chi-restraints excluded: chain H residue 653 CYS Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 211 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 103 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.200748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157995 restraints weight = 11888.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158852 restraints weight = 13113.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160287 restraints weight = 12358.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.162142 restraints weight = 7107.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163186 restraints weight = 5987.980| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8896 Z= 0.102 Angle : 0.540 10.093 12075 Z= 0.274 Chirality : 0.043 0.245 1339 Planarity : 0.003 0.050 1531 Dihedral : 6.067 52.600 1440 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.93 % Allowed : 23.29 % Favored : 72.77 % 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: -0.61 (0.26), residues: 1066 helix: -0.26 (0.52), residues: 110 sheet: -0.22 (0.31), residues: 271 loop : -0.45 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 549 TYR 0.009 0.001 TYR H 717 PHE 0.015 0.001 PHE H 258 TRP 0.010 0.001 TRP H 66 HIS 0.001 0.000 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8849) covalent geometry : angle 0.52628 (11968) SS BOND : bond 0.00261 ( 34) SS BOND : angle 1.01238 ( 68) hydrogen bonds : bond 0.02639 ( 201) hydrogen bonds : angle 4.94018 ( 585) link_ALPHA1-2 : bond 0.00376 ( 2) link_ALPHA1-2 : angle 1.45536 ( 6) link_ALPHA1-3 : bond 0.01033 ( 1) link_ALPHA1-3 : angle 1.53470 ( 3) link_ALPHA1-6 : bond 0.00659 ( 1) link_ALPHA1-6 : angle 1.48041 ( 3) link_BETA1-4 : bond 0.00480 ( 4) link_BETA1-4 : angle 2.24676 ( 12) link_NAG-ASN : bond 0.00525 ( 5) link_NAG-ASN : angle 1.75320 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 TRP cc_start: 0.8931 (t-100) cc_final: 0.8188 (m100) REVERT: H 327 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7561 (t80) REVERT: H 443 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8543 (ptmm) REVERT: H 478 MET cc_start: 0.7594 (mmm) cc_final: 0.6699 (ptm) REVERT: H 565 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: H 581 GLU cc_start: 0.8434 (pm20) cc_final: 0.7880 (pm20) REVERT: H 720 MET cc_start: 0.8213 (tpp) cc_final: 0.7967 (tpp) REVERT: L 151 TYR cc_start: 0.8107 (t80) cc_final: 0.7593 (t80) REVERT: L 166 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8142 (pt0) outliers start: 38 outliers final: 23 residues processed: 137 average time/residue: 0.0779 time to fit residues: 15.7395 Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 404 CYS Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 443 LYS Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 515 CYS Chi-restraints excluded: chain H residue 532 CYS Chi-restraints excluded: chain H residue 565 GLU Chi-restraints excluded: chain H residue 601 CYS Chi-restraints excluded: chain H residue 607 THR Chi-restraints excluded: chain H residue 653 CYS Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 211 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 14 optimal weight: 7.9990 chunk 80 optimal weight: 0.0570 chunk 103 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.209730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163306 restraints weight = 11792.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162622 restraints weight = 11727.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164535 restraints weight = 11351.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166014 restraints weight = 6371.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167143 restraints weight = 5609.460| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8896 Z= 0.102 Angle : 0.541 8.699 12075 Z= 0.275 Chirality : 0.043 0.242 1339 Planarity : 0.003 0.049 1531 Dihedral : 5.894 52.755 1440 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.93 % Allowed : 23.19 % Favored : 72.88 % 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: -0.54 (0.25), residues: 1066 helix: -0.21 (0.52), residues: 110 sheet: -0.16 (0.31), residues: 262 loop : -0.42 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 549 TYR 0.037 0.001 TYR H 717 PHE 0.015 0.001 PHE H 258 TRP 0.013 0.001 TRP H 66 HIS 0.001 0.000 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8849) covalent geometry : angle 0.52449 (11968) SS BOND : bond 0.00271 ( 34) SS BOND : angle 1.27538 ( 68) hydrogen bonds : bond 0.02650 ( 201) hydrogen bonds : angle 5.11240 ( 585) link_ALPHA1-2 : bond 0.00395 ( 2) link_ALPHA1-2 : angle 1.43309 ( 6) link_ALPHA1-3 : bond 0.01096 ( 1) link_ALPHA1-3 : angle 1.49175 ( 3) link_ALPHA1-6 : bond 0.00830 ( 1) link_ALPHA1-6 : angle 1.39460 ( 3) link_BETA1-4 : bond 0.00527 ( 4) link_BETA1-4 : angle 2.22746 ( 12) link_NAG-ASN : bond 0.00502 ( 5) link_NAG-ASN : angle 1.67873 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 TRP cc_start: 0.8905 (t-100) cc_final: 0.8027 (m100) REVERT: H 327 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7477 (t80) REVERT: H 443 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8479 (ptmm) REVERT: H 472 GLN cc_start: 0.7660 (tt0) cc_final: 0.7288 (tm-30) REVERT: H 537 ASN cc_start: 0.7872 (p0) cc_final: 0.7240 (p0) REVERT: H 565 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: H 720 MET cc_start: 0.8278 (tpp) cc_final: 0.8002 (tpp) REVERT: L 151 TYR cc_start: 0.8070 (t80) cc_final: 0.7564 (t80) outliers start: 38 outliers final: 27 residues processed: 134 average time/residue: 0.0932 time to fit residues: 17.5800 Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 404 CYS Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 443 LYS Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 515 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 532 CYS Chi-restraints excluded: chain H residue 565 GLU Chi-restraints excluded: chain H residue 567 SER Chi-restraints excluded: chain H residue 601 CYS Chi-restraints excluded: chain H residue 607 THR Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 199 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 37 optimal weight: 0.0770 chunk 63 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.209428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.162709 restraints weight = 11812.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164162 restraints weight = 11996.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.165142 restraints weight = 11579.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.167092 restraints weight = 6766.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168237 restraints weight = 5661.823| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8896 Z= 0.104 Angle : 0.539 8.037 12075 Z= 0.273 Chirality : 0.043 0.241 1339 Planarity : 0.003 0.048 1531 Dihedral : 5.661 52.547 1440 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.93 % Allowed : 23.19 % Favored : 72.88 % 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: -0.57 (0.26), residues: 1066 helix: -0.22 (0.52), residues: 110 sheet: -0.12 (0.31), residues: 271 loop : -0.47 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 549 TYR 0.032 0.001 TYR H 717 PHE 0.015 0.001 PHE H 258 TRP 0.011 0.001 TRP H 66 HIS 0.002 0.000 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8849) covalent geometry : angle 0.52573 (11968) SS BOND : bond 0.00299 ( 34) SS BOND : angle 1.01025 ( 68) hydrogen bonds : bond 0.02705 ( 201) hydrogen bonds : angle 4.92088 ( 585) link_ALPHA1-2 : bond 0.00381 ( 2) link_ALPHA1-2 : angle 1.44426 ( 6) link_ALPHA1-3 : bond 0.01007 ( 1) link_ALPHA1-3 : angle 1.67347 ( 3) link_ALPHA1-6 : bond 0.00770 ( 1) link_ALPHA1-6 : angle 1.44330 ( 3) link_BETA1-4 : bond 0.00544 ( 4) link_BETA1-4 : angle 2.24944 ( 12) link_NAG-ASN : bond 0.00513 ( 5) link_NAG-ASN : angle 1.67206 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 TRP cc_start: 0.8944 (t-100) cc_final: 0.8695 (t-100) REVERT: H 251 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.5153 (m-80) REVERT: H 327 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7440 (t80) REVERT: H 443 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8557 (ptmm) REVERT: H 472 GLN cc_start: 0.7546 (tt0) cc_final: 0.7208 (tm-30) REVERT: H 537 ASN cc_start: 0.7777 (p0) cc_final: 0.7118 (p0) REVERT: H 720 MET cc_start: 0.8281 (tpp) cc_final: 0.8019 (tpp) REVERT: L 151 TYR cc_start: 0.8040 (t80) cc_final: 0.7540 (t80) REVERT: L 166 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8158 (pt0) outliers start: 38 outliers final: 25 residues processed: 133 average time/residue: 0.0841 time to fit residues: 16.0890 Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 404 CYS Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 443 LYS Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 515 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 532 CYS Chi-restraints excluded: chain H residue 567 SER Chi-restraints excluded: chain H residue 601 CYS Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.208968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.162208 restraints weight = 11759.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161024 restraints weight = 11995.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163434 restraints weight = 11326.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.164770 restraints weight = 6747.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.167027 restraints weight = 5980.986| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8896 Z= 0.112 Angle : 0.555 11.906 12075 Z= 0.280 Chirality : 0.043 0.243 1339 Planarity : 0.003 0.048 1531 Dihedral : 5.558 52.558 1440 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.42 % Allowed : 23.91 % Favored : 72.67 % 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: -0.54 (0.25), residues: 1066 helix: -0.25 (0.52), residues: 110 sheet: 0.01 (0.32), residues: 261 loop : -0.49 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 549 TYR 0.030 0.001 TYR H 717 PHE 0.015 0.001 PHE H 258 TRP 0.009 0.001 TRP L 223 HIS 0.002 0.000 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8849) covalent geometry : angle 0.54068 (11968) SS BOND : bond 0.00238 ( 34) SS BOND : angle 1.10287 ( 68) hydrogen bonds : bond 0.02773 ( 201) hydrogen bonds : angle 4.94159 ( 585) link_ALPHA1-2 : bond 0.00343 ( 2) link_ALPHA1-2 : angle 1.42787 ( 6) link_ALPHA1-3 : bond 0.00985 ( 1) link_ALPHA1-3 : angle 1.67500 ( 3) link_ALPHA1-6 : bond 0.00731 ( 1) link_ALPHA1-6 : angle 1.44524 ( 3) link_BETA1-4 : bond 0.00561 ( 4) link_BETA1-4 : angle 2.27073 ( 12) link_NAG-ASN : bond 0.00522 ( 5) link_NAG-ASN : angle 1.68684 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 118 ASP cc_start: 0.8155 (t0) cc_final: 0.7935 (t0) REVERT: H 220 PHE cc_start: 0.8178 (m-10) cc_final: 0.7978 (m-10) REVERT: H 251 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5173 (m-80) REVERT: H 327 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7421 (t80) REVERT: H 443 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8537 (ptmm) REVERT: H 478 MET cc_start: 0.7678 (mmm) cc_final: 0.6733 (ptm) REVERT: H 537 ASN cc_start: 0.7841 (p0) cc_final: 0.7200 (p0) REVERT: H 581 GLU cc_start: 0.8487 (pm20) cc_final: 0.7988 (pm20) REVERT: H 720 MET cc_start: 0.8286 (tpp) cc_final: 0.7453 (tpp) REVERT: L 151 TYR cc_start: 0.8044 (t80) cc_final: 0.7529 (t80) REVERT: L 166 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8168 (pt0) outliers start: 33 outliers final: 29 residues processed: 129 average time/residue: 0.0801 time to fit residues: 15.0814 Evaluate side-chains 136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 320 ASP Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 395 CYS Chi-restraints excluded: chain H residue 404 CYS Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 443 LYS Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 515 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 532 CYS Chi-restraints excluded: chain H residue 565 GLU Chi-restraints excluded: chain H residue 567 SER Chi-restraints excluded: chain H residue 601 CYS Chi-restraints excluded: chain H residue 654 LEU Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 201 TYR Chi-restraints excluded: chain L residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 40.0000 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.206539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.160152 restraints weight = 11728.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.158101 restraints weight = 11946.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160615 restraints weight = 11624.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161818 restraints weight = 6795.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163297 restraints weight = 6091.942| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8896 Z= 0.148 Angle : 0.574 11.332 12075 Z= 0.290 Chirality : 0.044 0.248 1339 Planarity : 0.003 0.048 1531 Dihedral : 5.667 52.755 1440 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.52 % Allowed : 24.02 % Favored : 72.46 % 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: -0.62 (0.25), residues: 1066 helix: -0.24 (0.52), residues: 110 sheet: -0.10 (0.31), residues: 261 loop : -0.53 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 549 TYR 0.029 0.001 TYR H 717 PHE 0.016 0.001 PHE H 258 TRP 0.011 0.002 TRP L 223 HIS 0.003 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8849) covalent geometry : angle 0.55881 (11968) SS BOND : bond 0.00303 ( 34) SS BOND : angle 1.20206 ( 68) hydrogen bonds : bond 0.02884 ( 201) hydrogen bonds : angle 4.99160 ( 585) link_ALPHA1-2 : bond 0.00295 ( 2) link_ALPHA1-2 : angle 1.43563 ( 6) link_ALPHA1-3 : bond 0.00839 ( 1) link_ALPHA1-3 : angle 1.62960 ( 3) link_ALPHA1-6 : bond 0.00683 ( 1) link_ALPHA1-6 : angle 1.51227 ( 3) link_BETA1-4 : bond 0.00583 ( 4) link_BETA1-4 : angle 2.36330 ( 12) link_NAG-ASN : bond 0.00549 ( 5) link_NAG-ASN : angle 1.76405 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1356.08 seconds wall clock time: 24 minutes 13.13 seconds (1453.13 seconds total)