Starting phenix.real_space_refine on Fri Jul 3 10:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d99_30617/07_2026/7d99_30617.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d99_30617/07_2026/7d99_30617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2026/7d99_30617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2026/7d99_30617.map" model { file = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2026/7d99_30617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2026/7d99_30617.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2026/7d99_30617.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2026/7d99_30617.cif" } resolution = 2.9 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= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 104 5.16 5 Cl 4 4.86 5 C 8904 2.51 5 N 2314 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13800 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6841 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 34, 'TRANS': 856} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, D, E, F Time building chain proxies: 5.84, per 1000 atoms: 0.42 Number of scatterers: 13800 At special positions: 0 Unit cell: (112.554, 128.778, 149.058, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 104 16.00 O 2472 8.00 N 2314 7.00 C 8904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 352 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 360 " " NAG E 1 " - " ASN B 312 " " NAG F 1 " - " ASN B 360 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 615.9 milliseconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3252 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 6 sheets defined 60.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.862A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.744A pdb=" N GLU A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 164 removed outlier: 6.563A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LEU A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.613A pdb=" N SER A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.580A pdb=" N ARG A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 228 removed outlier: 4.277A pdb=" N PHE A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 242 through 269 removed outlier: 3.602A pdb=" N MET A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 removed outlier: 3.637A pdb=" N LYS A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 301 removed outlier: 3.603A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 287 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.705A pdb=" N GLY A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 removed outlier: 3.534A pdb=" N ILE A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 359' Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.717A pdb=" N LEU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.541A pdb=" N ALA A 436 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 438 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 439 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 475 Proline residue: A 452 - end of helix removed outlier: 3.556A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.866A pdb=" N GLY A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.642A pdb=" N LEU A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 525 removed outlier: 3.556A pdb=" N THR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.550A pdb=" N LEU A 529 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.706A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 removed outlier: 3.556A pdb=" N VAL A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 3.780A pdb=" N PHE A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.648A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 659 Processing helix chain 'A' and resid 663 through 681 removed outlier: 3.795A pdb=" N SER A 669 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 679 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 719 removed outlier: 3.853A pdb=" N SER A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 756 removed outlier: 3.605A pdb=" N GLU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.691A pdb=" N MET A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 775 " --> pdb=" O ARG A 771 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 removed outlier: 3.994A pdb=" N SER A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 809 " --> pdb=" O PRO A 805 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.563A pdb=" N PHE A 834 " --> pdb=" O VAL A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 866 removed outlier: 3.784A pdb=" N LEU A 858 " --> pdb=" O ASP A 854 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Proline residue: A 862 - end of helix Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 896 through 902 removed outlier: 3.659A pdb=" N TYR A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1031 removed outlier: 3.661A pdb=" N THR A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A1029 " --> pdb=" O GLY A1025 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A1030 " --> pdb=" O VAL A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1062 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.862A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.744A pdb=" N GLU B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 164 removed outlier: 6.563A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LEU B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.613A pdb=" N SER B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.580A pdb=" N ARG B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 228 removed outlier: 4.277A pdb=" N PHE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 242 through 269 removed outlier: 3.602A pdb=" N MET B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 removed outlier: 3.637A pdb=" N LYS B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 301 removed outlier: 3.603A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 287 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.705A pdb=" N GLY B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.534A pdb=" N ILE B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 359' Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.717A pdb=" N LEU B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.541A pdb=" N ALA B 436 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 475 Proline residue: B 452 - end of helix removed outlier: 3.556A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.866A pdb=" N GLY B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 488' Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.642A pdb=" N LEU B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 500 " --> pdb=" O ILE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 525 removed outlier: 3.556A pdb=" N THR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 removed outlier: 3.550A pdb=" N LEU B 529 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.706A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 602 removed outlier: 3.556A pdb=" N VAL B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix removed outlier: 3.780A pdb=" N PHE B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.648A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 622 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 659 Processing helix chain 'B' and resid 663 through 681 removed outlier: 3.795A pdb=" N SER B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 679 " --> pdb=" O TYR B 675 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 681 " --> pdb=" O LEU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 719 removed outlier: 3.853A pdb=" N SER B 713 " --> pdb=" O PRO B 709 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 756 removed outlier: 3.605A pdb=" N GLU B 747 " --> pdb=" O GLN B 743 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 781 removed outlier: 3.691A pdb=" N MET B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 removed outlier: 3.994A pdb=" N SER B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 812 " --> pdb=" O TRP B 808 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 815 " --> pdb=" O PHE B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 removed outlier: 3.563A pdb=" N PHE B 834 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 866 removed outlier: 3.784A pdb=" N LEU B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 860 " --> pdb=" O GLY B 856 " (cutoff:3.500A) Proline residue: B 862 - end of helix Processing helix chain 'B' and resid 887 through 896 Processing helix chain 'B' and resid 896 through 902 removed outlier: 3.659A pdb=" N TYR B 900 " --> pdb=" O GLN B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1031 removed outlier: 3.661A pdb=" N THR B1019 " --> pdb=" O ARG B1015 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B1029 " --> pdb=" O GLY B1025 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B1030 " --> pdb=" O VAL B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1062 Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.792A pdb=" N ARG A 313 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767 removed outlier: 4.298A pdb=" N VAL A 730 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA A 794 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A1068 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A1037 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A1071 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A1039 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS A 845 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU A1038 " --> pdb=" O HIS A 845 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP A 847 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ASN A1040 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N TRP A 849 " --> pdb=" O ASN A1040 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.792A pdb=" N ARG B 313 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA6, first strand: chain 'B' and resid 761 through 767 removed outlier: 4.298A pdb=" N VAL B 730 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA B 794 " --> pdb=" O MET B 697 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B1068 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B1037 " --> pdb=" O LEU B1069 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL B1071 " --> pdb=" O VAL B1037 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B1039 " --> pdb=" O VAL B1071 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS B 845 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU B1038 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP B 847 " --> pdb=" O LEU B1038 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ASN B1040 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N TRP B 849 " --> pdb=" O ASN B1040 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1992 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: 1.87 Time building geometry restraints manager: 1.34 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: 4368 1.34 - 1.47: 3474 1.47 - 1.60: 6092 1.60 - 1.72: 0 1.72 - 1.85: 164 Bond restraints: 14098 Sorted by residual: bond pdb=" C PHE B 428 " pdb=" N PRO B 429 " ideal model delta sigma weight residual 1.337 1.376 -0.039 9.80e-03 1.04e+04 1.59e+01 bond pdb=" C PHE A 428 " pdb=" N PRO A 429 " ideal model delta sigma weight residual 1.337 1.376 -0.039 9.80e-03 1.04e+04 1.59e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 14093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 17988 2.05 - 4.11: 988 4.11 - 6.16: 106 6.16 - 8.21: 40 8.21 - 10.26: 22 Bond angle restraints: 19144 Sorted by residual: angle pdb=" N GLY A 664 " pdb=" CA GLY A 664 " pdb=" C GLY A 664 " ideal model delta sigma weight residual 112.73 121.09 -8.36 1.20e+00 6.94e-01 4.85e+01 angle pdb=" N GLY B 664 " pdb=" CA GLY B 664 " pdb=" C GLY B 664 " ideal model delta sigma weight residual 112.73 121.09 -8.36 1.20e+00 6.94e-01 4.85e+01 angle pdb=" N GLU B 391 " pdb=" CA GLU B 391 " pdb=" C GLU B 391 " ideal model delta sigma weight residual 110.42 118.81 -8.39 1.55e+00 4.16e-01 2.93e+01 angle pdb=" N GLU A 391 " pdb=" CA GLU A 391 " pdb=" C GLU A 391 " ideal model delta sigma weight residual 110.42 118.81 -8.39 1.55e+00 4.16e-01 2.93e+01 angle pdb=" N GLY B 784 " pdb=" CA GLY B 784 " pdb=" C GLY B 784 " ideal model delta sigma weight residual 111.02 120.72 -9.70 1.86e+00 2.89e-01 2.72e+01 ... (remaining 19139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.35: 7752 14.35 - 28.70: 370 28.70 - 43.05: 104 43.05 - 57.41: 8 57.41 - 71.76: 6 Dihedral angle restraints: 8240 sinusoidal: 3158 harmonic: 5082 Sorted by residual: dihedral pdb=" CB CYS B 308 " pdb=" SG CYS B 308 " pdb=" SG CYS B 323 " pdb=" CB CYS B 323 " ideal model delta sinusoidal sigma weight residual -86.00 -148.72 62.72 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 323 " pdb=" CB CYS A 323 " ideal model delta sinusoidal sigma weight residual -86.00 -148.72 62.72 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CA GLU A 703 " pdb=" C GLU A 703 " pdb=" N GLN A 704 " pdb=" CA GLN A 704 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 8237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1586 0.053 - 0.106: 488 0.106 - 0.159: 130 0.159 - 0.212: 20 0.212 - 0.265: 12 Chirality restraints: 2236 Sorted by residual: chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2233 not shown) Planarity restraints: 2396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 539 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO A 540 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 540 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 540 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 539 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO B 540 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 540 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 540 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 804 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO B 805 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 805 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 805 " -0.037 5.00e-02 4.00e+02 ... (remaining 2393 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 3328 2.78 - 3.37: 13748 3.37 - 3.96: 24558 3.96 - 4.55: 34575 4.55 - 5.14: 52811 Nonbonded interactions: 129020 Sorted by model distance: nonbonded pdb=" O ASN A 331 " pdb=" OD1 ASN A 332 " model vdw 2.187 3.040 nonbonded pdb=" O ASN B 331 " pdb=" OD1 ASN B 332 " model vdw 2.187 3.040 nonbonded pdb=" OE1 GLU A 152 " pdb=" OH TYR A 383 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU B 152 " pdb=" OH TYR B 383 " model vdw 2.277 3.040 nonbonded pdb=" OG SER B 713 " pdb=" OE1 GLU B 756 " model vdw 2.293 3.040 ... (remaining 129015 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.790 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.009 0.080 14112 Z= 0.369 Angle : 1.119 12.302 19180 Z= 0.624 Chirality : 0.057 0.265 2236 Planarity : 0.007 0.069 2392 Dihedral : 9.644 71.758 4970 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.14 % Rotamer: Outliers : 0.41 % Allowed : 2.18 % Favored : 97.41 % 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: -5.36 (0.14), residues: 1770 helix: -4.44 (0.07), residues: 896 sheet: -0.41 (0.42), residues: 140 loop : -2.80 (0.18), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 674 TYR 0.021 0.003 TYR A 466 PHE 0.038 0.004 PHE B 761 TRP 0.024 0.003 TRP A 339 HIS 0.012 0.002 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.37 (14098) covalent geometry : angle 1.09486 / 0.62 (19144) SS BOND : bond 0.00303 / 0.18 ( 6) SS BOND : angle 2.92883 / 1.62 ( 12) hydrogen bonds : bond 0.31965 / 21.14 ( 678) hydrogen bonds : angle 10.44993 / 7.14 ( 1992) link_BETA1-4 : bond 0.00339 / 0.16 ( 4) link_BETA1-4 : angle 7.53535 / 4.40 ( 12) link_NAG-ASN : bond 0.01329 / 0.65 ( 4) link_NAG-ASN : angle 5.02570 / 2.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 309 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8055 (mmt) cc_final: 0.7683 (mmt) REVERT: B 435 MET cc_start: 0.8054 (mmt) cc_final: 0.7699 (mmt) outliers start: 6 outliers final: 2 residues processed: 311 average time/residue: 0.6055 time to fit residues: 204.1301 Evaluate side-chains 161 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN A 250 ASN A 330 HIS A 359 ASN A 547 HIS A 615 HIS ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS A 868 HIS A1024 ASN B 236 GLN B 250 ASN B 330 HIS B 359 ASN B 547 HIS B 615 HIS ** B 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 HIS B 868 HIS B1024 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.149289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105936 restraints weight = 16351.537| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.14 r_work: 0.2971 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14112 Z= 0.133 Angle : 0.689 10.914 19180 Z= 0.344 Chirality : 0.044 0.226 2236 Planarity : 0.005 0.057 2392 Dihedral : 5.263 25.824 1908 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.73 % Allowed : 11.87 % Favored : 85.40 % 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: -2.65 (0.17), residues: 1770 helix: -1.65 (0.14), residues: 944 sheet: 0.33 (0.46), residues: 130 loop : -2.18 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 877 TYR 0.011 0.001 TYR B 427 PHE 0.016 0.001 PHE A 761 TRP 0.015 0.001 TRP B 661 HIS 0.009 0.001 HIS B1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (14098) covalent geometry : angle 0.67172 / 0.34 (19144) SS BOND : bond 0.00284 / 0.15 ( 6) SS BOND : angle 1.39479 / 0.77 ( 12) hydrogen bonds : bond 0.06015 / 3.96 ( 678) hydrogen bonds : angle 4.76428 / 3.17 ( 1992) link_BETA1-4 : bond 0.00441 / 0.20 ( 4) link_BETA1-4 : angle 4.36452 / 2.53 ( 12) link_NAG-ASN : bond 0.00263 / 0.13 ( 4) link_NAG-ASN : angle 4.18827 / 2.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.7603 (tt0) cc_final: 0.7280 (tp30) REVERT: A 358 GLN cc_start: 0.8283 (mt0) cc_final: 0.7975 (mt0) REVERT: A 443 ASP cc_start: 0.8561 (m-30) cc_final: 0.8323 (m-30) REVERT: A 536 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: A 583 MET cc_start: 0.9039 (tpp) cc_final: 0.8831 (mmt) REVERT: A 747 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: A 774 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: B 354 GLU cc_start: 0.7595 (tt0) cc_final: 0.7269 (tp30) REVERT: B 358 GLN cc_start: 0.8256 (mt0) cc_final: 0.7958 (mt0) REVERT: B 443 ASP cc_start: 0.8546 (m-30) cc_final: 0.8309 (m-30) REVERT: B 536 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: B 583 MET cc_start: 0.9052 (tpp) cc_final: 0.8838 (mmt) REVERT: B 747 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: B 774 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8138 (mpp) outliers start: 40 outliers final: 8 residues processed: 212 average time/residue: 0.5724 time to fit residues: 132.9079 Evaluate side-chains 169 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 774 MET Chi-restraints excluded: chain B residue 1018 HIS Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 36 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 599 GLN A 776 HIS A 789 ASN B 599 GLN B 776 HIS B 789 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.149148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106934 restraints weight = 16518.792| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.20 r_work: 0.2942 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14112 Z= 0.122 Angle : 0.614 14.235 19180 Z= 0.299 Chirality : 0.042 0.191 2236 Planarity : 0.004 0.054 2392 Dihedral : 5.488 86.043 1908 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.62 % Allowed : 12.21 % Favored : 84.17 % 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: -1.17 (0.19), residues: 1770 helix: -0.11 (0.17), residues: 960 sheet: 0.53 (0.46), residues: 130 loop : -1.97 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 317 TYR 0.009 0.001 TYR B 636 PHE 0.015 0.001 PHE A 761 TRP 0.010 0.001 TRP A 661 HIS 0.008 0.001 HIS B1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (14098) covalent geometry : angle 0.59724 / 0.30 (19144) SS BOND : bond 0.00264 / 0.13 ( 6) SS BOND : angle 1.19855 / 0.66 ( 12) hydrogen bonds : bond 0.04632 / 3.03 ( 678) hydrogen bonds : angle 4.13929 / 2.74 ( 1992) link_BETA1-4 : bond 0.00472 / 0.21 ( 4) link_BETA1-4 : angle 3.65734 / 2.12 ( 12) link_NAG-ASN : bond 0.00300 / 0.15 ( 4) link_NAG-ASN : angle 4.35151 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.8694 (m-30) cc_final: 0.8407 (m-30) REVERT: A 509 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 536 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: A 583 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8827 (mmt) REVERT: A 691 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7351 (tpp80) REVERT: A 732 GLU cc_start: 0.8454 (pt0) cc_final: 0.8211 (mt-10) REVERT: A 747 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: A 770 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8668 (tt) REVERT: A 783 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8409 (pp) REVERT: A 1016 ARG cc_start: 0.5837 (mtt180) cc_final: 0.5611 (mtt180) REVERT: B 443 ASP cc_start: 0.8686 (m-30) cc_final: 0.8396 (m-30) REVERT: B 509 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8451 (mm) REVERT: B 536 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: B 583 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8834 (mmt) REVERT: B 691 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7323 (tpp80) REVERT: B 747 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: B 770 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8672 (tt) REVERT: B 783 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8429 (pp) REVERT: B 1016 ARG cc_start: 0.5826 (mtt180) cc_final: 0.5602 (mtt180) outliers start: 53 outliers final: 14 residues processed: 204 average time/residue: 0.5114 time to fit residues: 115.0793 Evaluate side-chains 182 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.145947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103660 restraints weight = 16535.963| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.14 r_work: 0.2816 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14112 Z= 0.160 Angle : 0.640 16.303 19180 Z= 0.308 Chirality : 0.044 0.188 2236 Planarity : 0.004 0.059 2392 Dihedral : 5.553 93.987 1908 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.50 % Allowed : 11.66 % Favored : 83.83 % 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 (0.19), residues: 1770 helix: 0.38 (0.17), residues: 942 sheet: 0.71 (0.47), residues: 130 loop : -1.87 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 750 TYR 0.013 0.001 TYR B 636 PHE 0.020 0.002 PHE B 761 TRP 0.009 0.001 TRP B 380 HIS 0.011 0.001 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (14098) covalent geometry : angle 0.62375 / 0.30 (19144) SS BOND : bond 0.00347 / 0.18 ( 6) SS BOND : angle 1.46583 / 0.82 ( 12) hydrogen bonds : bond 0.04688 / 3.08 ( 678) hydrogen bonds : angle 4.10937 / 2.72 ( 1992) link_BETA1-4 : bond 0.00429 / 0.20 ( 4) link_BETA1-4 : angle 3.13265 / 1.82 ( 12) link_NAG-ASN : bond 0.00180 / 0.09 ( 4) link_NAG-ASN : angle 4.62067 / 2.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8532 (t70) cc_final: 0.8145 (t0) REVERT: A 443 ASP cc_start: 0.8604 (m-30) cc_final: 0.8259 (m-30) REVERT: A 509 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8320 (mm) REVERT: A 536 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: A 543 GLN cc_start: 0.8395 (tt0) cc_final: 0.8137 (tm-30) REVERT: A 583 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8782 (mmt) REVERT: A 691 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7364 (tpp80) REVERT: A 732 GLU cc_start: 0.8414 (pt0) cc_final: 0.8163 (mt-10) REVERT: A 747 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: A 770 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 838 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7447 (pp30) REVERT: A 878 ILE cc_start: 0.8083 (mt) cc_final: 0.7827 (tt) REVERT: A 1016 ARG cc_start: 0.5922 (mtt180) cc_final: 0.5647 (mtt180) REVERT: A 1017 MET cc_start: 0.7958 (tpp) cc_final: 0.7494 (tpp) REVERT: A 1060 VAL cc_start: 0.8466 (t) cc_final: 0.8239 (t) REVERT: B 443 ASP cc_start: 0.8604 (m-30) cc_final: 0.8261 (m-30) REVERT: B 509 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8329 (mm) REVERT: B 536 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: B 543 GLN cc_start: 0.8381 (tt0) cc_final: 0.8121 (tm-30) REVERT: B 583 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8779 (mmt) REVERT: B 691 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7366 (tpp80) REVERT: B 747 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: B 770 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8622 (tt) REVERT: B 783 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8685 (pp) REVERT: B 1017 MET cc_start: 0.7954 (tpp) cc_final: 0.7500 (tpp) REVERT: B 1060 VAL cc_start: 0.8467 (t) cc_final: 0.8243 (t) outliers start: 66 outliers final: 17 residues processed: 212 average time/residue: 0.5243 time to fit residues: 122.7270 Evaluate side-chains 188 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 163 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1018 HIS B1018 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105995 restraints weight = 16447.664| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.17 r_work: 0.2946 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14112 Z= 0.114 Angle : 0.588 15.892 19180 Z= 0.281 Chirality : 0.042 0.182 2236 Planarity : 0.004 0.059 2392 Dihedral : 5.301 89.022 1908 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.41 % Allowed : 12.89 % Favored : 83.70 % 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: -0.28 (0.20), residues: 1770 helix: 0.74 (0.17), residues: 960 sheet: 0.82 (0.47), residues: 130 loop : -1.75 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 750 TYR 0.010 0.001 TYR B 636 PHE 0.012 0.001 PHE B 541 TRP 0.011 0.001 TRP B 661 HIS 0.013 0.001 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (14098) covalent geometry : angle 0.57255 / 0.28 (19144) SS BOND : bond 0.00267 / 0.14 ( 6) SS BOND : angle 1.10778 / 0.62 ( 12) hydrogen bonds : bond 0.03988 / 2.61 ( 678) hydrogen bonds : angle 3.91141 / 2.60 ( 1992) link_BETA1-4 : bond 0.00445 / 0.21 ( 4) link_BETA1-4 : angle 3.03169 / 1.76 ( 12) link_NAG-ASN : bond 0.00255 / 0.12 ( 4) link_NAG-ASN : angle 4.30765 / 2.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (pp) REVERT: A 415 ASP cc_start: 0.8611 (t70) cc_final: 0.8281 (t0) REVERT: A 536 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: A 543 GLN cc_start: 0.8449 (tt0) cc_final: 0.8172 (tm-30) REVERT: A 547 HIS cc_start: 0.8014 (m90) cc_final: 0.7632 (m-70) REVERT: A 583 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8802 (mmt) REVERT: A 691 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7267 (tpp80) REVERT: A 838 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7490 (pp30) REVERT: A 845 HIS cc_start: 0.7022 (m170) cc_final: 0.6807 (m170) REVERT: A 1060 VAL cc_start: 0.8574 (t) cc_final: 0.8335 (t) REVERT: A 1077 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: B 315 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8244 (pp) REVERT: B 443 ASP cc_start: 0.8677 (m-30) cc_final: 0.8323 (m-30) REVERT: B 536 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8446 (m-30) REVERT: B 543 GLN cc_start: 0.8438 (tt0) cc_final: 0.8160 (tm-30) REVERT: B 547 HIS cc_start: 0.7999 (m90) cc_final: 0.7556 (m-70) REVERT: B 583 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8803 (mmt) REVERT: B 691 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7264 (tpp80) REVERT: B 783 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8549 (pp) REVERT: B 838 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7471 (pp30) REVERT: B 845 HIS cc_start: 0.7004 (m170) cc_final: 0.6769 (m170) REVERT: B 1060 VAL cc_start: 0.8562 (t) cc_final: 0.8333 (t) REVERT: B 1077 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7401 (mt-10) outliers start: 50 outliers final: 16 residues processed: 213 average time/residue: 0.5507 time to fit residues: 129.4508 Evaluate side-chains 197 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 722 LYS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 35 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 14 optimal weight: 0.0000 chunk 112 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 439 ASN A1018 HIS B 94 ASN B 236 GLN B 439 ASN B1018 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.102488 restraints weight = 16410.762| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.17 r_work: 0.2818 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14112 Z= 0.138 Angle : 0.606 16.048 19180 Z= 0.293 Chirality : 0.043 0.180 2236 Planarity : 0.004 0.060 2392 Dihedral : 5.345 92.279 1908 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.75 % Allowed : 12.62 % Favored : 83.63 % 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: -0.11 (0.20), residues: 1770 helix: 0.97 (0.17), residues: 942 sheet: 0.77 (0.46), residues: 130 loop : -1.74 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 750 TYR 0.011 0.001 TYR A 636 PHE 0.013 0.001 PHE A 834 TRP 0.009 0.001 TRP B 661 HIS 0.009 0.001 HIS B1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (14098) covalent geometry : angle 0.59048 / 0.29 (19144) SS BOND : bond 0.00846 / 0.51 ( 6) SS BOND : angle 1.95680 / 1.09 ( 12) hydrogen bonds : bond 0.04223 / 2.78 ( 678) hydrogen bonds : angle 3.92525 / 2.61 ( 1992) link_BETA1-4 : bond 0.00385 / 0.18 ( 4) link_BETA1-4 : angle 2.82161 / 1.64 ( 12) link_NAG-ASN : bond 0.00188 / 0.09 ( 4) link_NAG-ASN : angle 4.42840 / 2.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8617 (t70) cc_final: 0.8268 (t0) REVERT: A 443 ASP cc_start: 0.8603 (m-30) cc_final: 0.8375 (m-30) REVERT: A 536 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: A 543 GLN cc_start: 0.8354 (tt0) cc_final: 0.8081 (tm-30) REVERT: A 547 HIS cc_start: 0.7876 (m90) cc_final: 0.7427 (m-70) REVERT: A 583 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8727 (mmt) REVERT: A 691 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7261 (tpp80) REVERT: A 731 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8241 (pt) REVERT: A 746 GLU cc_start: 0.8170 (tt0) cc_final: 0.7900 (tt0) REVERT: A 747 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: A 838 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7532 (pp30) REVERT: A 845 HIS cc_start: 0.6966 (m170) cc_final: 0.6747 (m170) REVERT: A 1060 VAL cc_start: 0.8500 (t) cc_final: 0.8262 (t) REVERT: A 1077 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: B 536 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8405 (m-30) REVERT: B 543 GLN cc_start: 0.8340 (tt0) cc_final: 0.8044 (tm-30) REVERT: B 547 HIS cc_start: 0.7848 (m90) cc_final: 0.7398 (m-70) REVERT: B 583 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8726 (mmt) REVERT: B 691 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7238 (tpp80) REVERT: B 746 GLU cc_start: 0.8278 (tt0) cc_final: 0.8002 (tt0) REVERT: B 747 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: B 783 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8675 (pp) REVERT: B 838 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7495 (pp30) REVERT: B 845 HIS cc_start: 0.6995 (m170) cc_final: 0.6743 (m170) REVERT: B 1060 VAL cc_start: 0.8488 (t) cc_final: 0.8254 (t) REVERT: B 1077 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7338 (mt-10) outliers start: 55 outliers final: 20 residues processed: 207 average time/residue: 0.5800 time to fit residues: 131.9365 Evaluate side-chains 199 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 722 LYS Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1018 HIS B 789 ASN B1018 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102347 restraints weight = 16546.418| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.17 r_work: 0.2792 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14112 Z= 0.138 Angle : 0.607 16.432 19180 Z= 0.292 Chirality : 0.043 0.185 2236 Planarity : 0.004 0.060 2392 Dihedral : 5.336 92.682 1908 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.82 % Allowed : 12.41 % Favored : 83.77 % 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: 0.07 (0.20), residues: 1770 helix: 1.14 (0.17), residues: 942 sheet: 0.89 (0.47), residues: 130 loop : -1.70 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 750 TYR 0.010 0.001 TYR B 636 PHE 0.012 0.001 PHE B 834 TRP 0.010 0.001 TRP A 850 HIS 0.010 0.001 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (14098) covalent geometry : angle 0.59146 / 0.29 (19144) SS BOND : bond 0.00385 / 0.21 ( 6) SS BOND : angle 1.96032 / 1.09 ( 12) hydrogen bonds : bond 0.04140 / 2.72 ( 678) hydrogen bonds : angle 3.90010 / 2.59 ( 1992) link_BETA1-4 : bond 0.00454 / 0.21 ( 4) link_BETA1-4 : angle 2.72353 / 1.58 ( 12) link_NAG-ASN : bond 0.00185 / 0.09 ( 4) link_NAG-ASN : angle 4.35979 / 2.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.8599 (t70) cc_final: 0.8266 (t0) REVERT: A 536 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: A 543 GLN cc_start: 0.8334 (tt0) cc_final: 0.8047 (tm-30) REVERT: A 583 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8704 (mmt) REVERT: A 691 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7182 (tpp80) REVERT: A 731 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8150 (pt) REVERT: A 746 GLU cc_start: 0.8095 (tt0) cc_final: 0.7884 (tt0) REVERT: A 838 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7302 (pp30) REVERT: A 840 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7822 (mpt90) REVERT: A 845 HIS cc_start: 0.6966 (m170) cc_final: 0.6747 (m170) REVERT: A 1048 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: A 1077 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: B 536 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: B 543 GLN cc_start: 0.8327 (tt0) cc_final: 0.8039 (tm-30) REVERT: B 583 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8716 (mmt) REVERT: B 691 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7190 (tpp80) REVERT: B 746 GLU cc_start: 0.8170 (tt0) cc_final: 0.7912 (tt0) REVERT: B 783 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8639 (pp) REVERT: B 838 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7394 (pp30) REVERT: B 840 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7820 (mpt90) REVERT: B 845 HIS cc_start: 0.6927 (m170) cc_final: 0.6631 (m170) REVERT: B 1077 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7366 (mt-10) outliers start: 56 outliers final: 22 residues processed: 204 average time/residue: 0.5315 time to fit residues: 119.8699 Evaluate side-chains 208 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 840 ARG Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 722 LYS Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 808 TRP Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 840 ARG Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 80 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1018 HIS B 699 ASN B1018 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104097 restraints weight = 16392.481| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.15 r_work: 0.2935 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14112 Z= 0.114 Angle : 0.588 15.963 19180 Z= 0.284 Chirality : 0.042 0.187 2236 Planarity : 0.004 0.062 2392 Dihedral : 5.338 97.556 1908 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.93 % Allowed : 13.30 % Favored : 83.77 % 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: 0.22 (0.20), residues: 1770 helix: 1.24 (0.17), residues: 962 sheet: 0.96 (0.47), residues: 134 loop : -1.69 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 483 TYR 0.009 0.001 TYR B 636 PHE 0.011 0.001 PHE B 541 TRP 0.012 0.001 TRP A 850 HIS 0.010 0.001 HIS B1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (14098) covalent geometry : angle 0.57418 / 0.28 (19144) SS BOND : bond 0.00341 / 0.18 ( 6) SS BOND : angle 1.67015 / 0.91 ( 12) hydrogen bonds : bond 0.03786 / 2.49 ( 678) hydrogen bonds : angle 3.81502 / 2.54 ( 1992) link_BETA1-4 : bond 0.00498 / 0.23 ( 4) link_BETA1-4 : angle 2.74438 / 1.59 ( 12) link_NAG-ASN : bond 0.00213 / 0.10 ( 4) link_NAG-ASN : angle 4.11755 / 2.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.8635 (m-30) cc_final: 0.8426 (m-30) REVERT: A 536 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: A 543 GLN cc_start: 0.8413 (tt0) cc_final: 0.8142 (tm-30) REVERT: A 583 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8770 (mmt) REVERT: A 691 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7193 (tpp80) REVERT: A 746 GLU cc_start: 0.8221 (tt0) cc_final: 0.7992 (tt0) REVERT: A 838 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7454 (pp30) REVERT: A 840 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7831 (mpt90) REVERT: A 845 HIS cc_start: 0.7032 (m170) cc_final: 0.6830 (m170) REVERT: A 1077 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: B 536 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: B 543 GLN cc_start: 0.8402 (tt0) cc_final: 0.8129 (tm-30) REVERT: B 583 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8774 (mmt) REVERT: B 691 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7202 (tpp80) REVERT: B 746 GLU cc_start: 0.8252 (tt0) cc_final: 0.7970 (tt0) REVERT: B 783 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 838 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7466 (pp30) REVERT: B 840 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7777 (mpt90) REVERT: B 845 HIS cc_start: 0.7011 (m170) cc_final: 0.6788 (m170) REVERT: B 1048 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7977 (ttm-80) REVERT: B 1077 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7427 (mt-10) outliers start: 43 outliers final: 13 residues processed: 205 average time/residue: 0.5216 time to fit residues: 117.9253 Evaluate side-chains 196 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 840 ARG Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 840 ARG Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1048 ARG Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 88 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 145 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 140 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 GLN A 699 ASN A1018 HIS B 365 GLN B 699 ASN B1018 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106190 restraints weight = 16530.090| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.19 r_work: 0.2941 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14112 Z= 0.108 Angle : 0.591 14.988 19180 Z= 0.284 Chirality : 0.041 0.197 2236 Planarity : 0.004 0.063 2392 Dihedral : 5.542 112.745 1908 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.73 % Allowed : 14.32 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1770 helix: 1.41 (0.17), residues: 964 sheet: 0.99 (0.47), residues: 134 loop : -1.64 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 483 TYR 0.009 0.001 TYR B 636 PHE 0.010 0.001 PHE A 541 TRP 0.016 0.001 TRP A 850 HIS 0.010 0.001 HIS B1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (14098) covalent geometry : angle 0.57774 / 0.28 (19144) SS BOND : bond 0.00323 / 0.17 ( 6) SS BOND : angle 1.51588 / 0.82 ( 12) hydrogen bonds : bond 0.03594 / 2.37 ( 678) hydrogen bonds : angle 3.72564 / 2.48 ( 1992) link_BETA1-4 : bond 0.00519 / 0.25 ( 4) link_BETA1-4 : angle 2.73408 / 1.58 ( 12) link_NAG-ASN : bond 0.00224 / 0.11 ( 4) link_NAG-ASN : angle 3.99482 / 2.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.8139 (mt) cc_final: 0.7862 (mp) REVERT: A 536 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: A 543 GLN cc_start: 0.8425 (tt0) cc_final: 0.8141 (tm-30) REVERT: A 547 HIS cc_start: 0.7920 (m90) cc_final: 0.7533 (m-70) REVERT: A 583 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8770 (mmt) REVERT: A 691 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7136 (tpp80) REVERT: A 746 GLU cc_start: 0.8259 (tt0) cc_final: 0.8055 (tt0) REVERT: A 838 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7456 (pp30) REVERT: A 840 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7799 (mpt90) REVERT: A 845 HIS cc_start: 0.7053 (m170) cc_final: 0.6842 (m170) REVERT: A 1016 ARG cc_start: 0.5862 (mtt180) cc_final: 0.5549 (mtt180) REVERT: A 1060 VAL cc_start: 0.8570 (t) cc_final: 0.8308 (t) REVERT: A 1077 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: B 536 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: B 543 GLN cc_start: 0.8405 (tt0) cc_final: 0.8129 (tm-30) REVERT: B 547 HIS cc_start: 0.7894 (m90) cc_final: 0.7447 (m-70) REVERT: B 691 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7133 (tpp80) REVERT: B 746 GLU cc_start: 0.8242 (tt0) cc_final: 0.8040 (tt0) REVERT: B 783 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8515 (pp) REVERT: B 845 HIS cc_start: 0.7050 (m170) cc_final: 0.6834 (m170) REVERT: B 1048 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8001 (ttm-80) REVERT: B 1060 VAL cc_start: 0.8547 (t) cc_final: 0.8290 (t) REVERT: B 1077 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7422 (mt-10) outliers start: 40 outliers final: 11 residues processed: 204 average time/residue: 0.5009 time to fit residues: 113.1443 Evaluate side-chains 198 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 840 ARG Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1048 ARG Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 699 ASN A1018 HIS B 699 ASN B1018 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106280 restraints weight = 16453.712| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.14 r_work: 0.2979 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14112 Z= 0.109 Angle : 0.595 14.272 19180 Z= 0.286 Chirality : 0.042 0.215 2236 Planarity : 0.004 0.062 2392 Dihedral : 4.123 20.264 1904 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.98 % Allowed : 15.69 % Favored : 82.33 % 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: 0.49 (0.20), residues: 1770 helix: 1.49 (0.17), residues: 962 sheet: 1.12 (0.47), residues: 132 loop : -1.63 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 872 TYR 0.009 0.001 TYR A 636 PHE 0.010 0.001 PHE A 541 TRP 0.017 0.001 TRP A 850 HIS 0.010 0.001 HIS B1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (14098) covalent geometry : angle 0.58206 / 0.28 (19144) SS BOND : bond 0.00306 / 0.16 ( 6) SS BOND : angle 1.49683 / 0.82 ( 12) hydrogen bonds : bond 0.03531 / 2.33 ( 678) hydrogen bonds : angle 3.69947 / 2.47 ( 1992) link_BETA1-4 : bond 0.00470 / 0.22 ( 4) link_BETA1-4 : angle 2.71826 / 1.58 ( 12) link_NAG-ASN : bond 0.00213 / 0.10 ( 4) link_NAG-ASN : angle 3.94437 / 2.23 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.8114 (mt) cc_final: 0.7838 (mp) REVERT: A 536 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: A 543 GLN cc_start: 0.8368 (tt0) cc_final: 0.8084 (tm-30) REVERT: A 547 HIS cc_start: 0.7887 (m90) cc_final: 0.7447 (m-70) REVERT: A 583 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8755 (mmt) REVERT: A 691 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7094 (tpp80) REVERT: A 746 GLU cc_start: 0.8202 (tt0) cc_final: 0.7963 (tt0) REVERT: A 747 GLU cc_start: 0.8102 (mp0) cc_final: 0.7786 (mp0) REVERT: A 845 HIS cc_start: 0.7066 (m170) cc_final: 0.6852 (m170) REVERT: A 1016 ARG cc_start: 0.5969 (mtt180) cc_final: 0.5697 (mtt180) REVERT: A 1060 VAL cc_start: 0.8573 (t) cc_final: 0.8314 (t) REVERT: A 1077 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: B 536 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: B 543 GLN cc_start: 0.8396 (tt0) cc_final: 0.8118 (tm-30) REVERT: B 547 HIS cc_start: 0.7886 (m90) cc_final: 0.7445 (m-70) REVERT: B 691 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7112 (tpp80) REVERT: B 746 GLU cc_start: 0.8188 (tt0) cc_final: 0.7938 (tt0) REVERT: B 747 GLU cc_start: 0.8136 (mp0) cc_final: 0.7825 (mp0) REVERT: B 783 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8495 (pp) REVERT: B 845 HIS cc_start: 0.7026 (m170) cc_final: 0.6803 (m170) REVERT: B 1016 ARG cc_start: 0.5993 (mtt180) cc_final: 0.5701 (mtt180) REVERT: B 1048 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8015 (ttm-80) REVERT: B 1060 VAL cc_start: 0.8590 (t) cc_final: 0.8328 (t) REVERT: B 1077 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7382 (mt-10) outliers start: 29 outliers final: 14 residues processed: 203 average time/residue: 0.5294 time to fit residues: 118.9747 Evaluate side-chains 207 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1048 ARG Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1018 HIS B 236 GLN B 853 HIS B1018 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102979 restraints weight = 16494.249| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.15 r_work: 0.2939 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14112 Z= 0.153 Angle : 0.642 14.981 19180 Z= 0.307 Chirality : 0.044 0.205 2236 Planarity : 0.004 0.060 2392 Dihedral : 4.245 21.442 1904 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.11 % Allowed : 15.83 % Favored : 82.06 % 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: 0.39 (0.20), residues: 1770 helix: 1.42 (0.17), residues: 954 sheet: 1.14 (0.47), residues: 132 loop : -1.66 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 483 TYR 0.011 0.001 TYR A 636 PHE 0.014 0.001 PHE B 761 TRP 0.018 0.001 TRP A 850 HIS 0.009 0.001 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (14098) covalent geometry : angle 0.62848 / 0.30 (19144) SS BOND : bond 0.00391 / 0.21 ( 6) SS BOND : angle 1.77553 / 0.99 ( 12) hydrogen bonds : bond 0.04185 / 2.76 ( 678) hydrogen bonds : angle 3.87111 / 2.58 ( 1992) link_BETA1-4 : bond 0.00460 / 0.21 ( 4) link_BETA1-4 : angle 2.56090 / 1.49 ( 12) link_NAG-ASN : bond 0.00101 / 0.05 ( 4) link_NAG-ASN : angle 4.30525 / 2.43 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4984.36 seconds wall clock time: 85 minutes 32.29 seconds (5132.29 seconds total)