Starting phenix.real_space_refine on Wed Mar 4 12:48:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d99_30617/03_2026/7d99_30617.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d99_30617/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7d99_30617/03_2026/7d99_30617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d99_30617/03_2026/7d99_30617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d99_30617/03_2026/7d99_30617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d99_30617/03_2026/7d99_30617.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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: 5.99, per 1000 atoms: 0.43 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: 1.29 Conformation dependent library (CDL) restraints added in 541.4 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: 0.50 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: 2.43 Time building geometry restraints manager: 1.74 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: 7892 14.35 - 28.70: 382 28.70 - 43.05: 112 43.05 - 57.41: 16 57.41 - 71.76: 6 Dihedral angle restraints: 8408 sinusoidal: 3326 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 8405 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: 0.03 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.070 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 9.923 71.758 5138 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 covalent geometry : bond 0.00888 (14098) covalent geometry : angle 1.09486 (19144) SS BOND : bond 0.00303 ( 6) SS BOND : angle 2.92883 ( 12) hydrogen bonds : bond 0.31965 ( 678) hydrogen bonds : angle 10.44993 ( 1992) link_BETA1-4 : bond 0.00339 ( 4) link_BETA1-4 : angle 7.53535 ( 12) link_NAG-ASN : bond 0.01329 ( 4) link_NAG-ASN : angle 5.02570 ( 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 : 0.451 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: 0.6775 time to fit residues: 227.3652 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3694 r_free = 0.3694 target = 0.149462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106173 restraints weight = 16354.610| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.19 r_work: 0.2857 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14112 Z= 0.133 Angle : 0.692 10.899 19180 Z= 0.345 Chirality : 0.044 0.228 2236 Planarity : 0.005 0.054 2392 Dihedral : 6.579 55.307 2076 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.86 % Allowed : 11.73 % 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: -2.75 (0.17), residues: 1770 helix: -1.75 (0.14), residues: 944 sheet: 0.32 (0.46), residues: 130 loop : -2.18 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 877 TYR 0.011 0.001 TYR B 427 PHE 0.015 0.001 PHE A 761 TRP 0.016 0.001 TRP B 661 HIS 0.010 0.001 HIS B1018 Details of bonding type rmsd covalent geometry : bond 0.00273 (14098) covalent geometry : angle 0.67224 (19144) SS BOND : bond 0.00292 ( 6) SS BOND : angle 1.40909 ( 12) hydrogen bonds : bond 0.06068 ( 678) hydrogen bonds : angle 4.77504 ( 1992) link_BETA1-4 : bond 0.00189 ( 4) link_BETA1-4 : angle 4.60858 ( 12) link_NAG-ASN : bond 0.00223 ( 4) link_NAG-ASN : angle 4.56843 ( 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 243 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.7698 (tt0) cc_final: 0.7243 (tp30) REVERT: A 358 GLN cc_start: 0.8279 (mt0) cc_final: 0.7885 (mt0) REVERT: A 435 MET cc_start: 0.8597 (mmt) cc_final: 0.8393 (mmt) REVERT: A 443 ASP cc_start: 0.8496 (m-30) cc_final: 0.8248 (m-30) REVERT: A 536 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8401 (m-30) REVERT: A 583 MET cc_start: 0.9000 (tpp) cc_final: 0.8793 (mmt) REVERT: A 747 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: A 774 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7993 (mpp) REVERT: A 1016 ARG cc_start: 0.5786 (mtt180) cc_final: 0.5475 (mtt180) REVERT: B 434 ILE cc_start: 0.8010 (mt) cc_final: 0.7804 (mp) REVERT: B 443 ASP cc_start: 0.8477 (m-30) cc_final: 0.8228 (m-30) REVERT: B 536 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8401 (m-30) REVERT: B 583 MET cc_start: 0.9008 (tpp) cc_final: 0.8797 (mmt) REVERT: B 747 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: B 774 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8013 (mpp) outliers start: 42 outliers final: 8 residues processed: 217 average time/residue: 0.6366 time to fit residues: 150.6345 Evaluate side-chains 173 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 1.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104244 restraints weight = 16549.601| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.20 r_work: 0.2850 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14112 Z= 0.138 Angle : 0.627 14.567 19180 Z= 0.304 Chirality : 0.043 0.191 2236 Planarity : 0.004 0.054 2392 Dihedral : 6.299 88.310 2076 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.68 % Allowed : 12.14 % 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: -1.24 (0.19), residues: 1770 helix: -0.20 (0.16), residues: 958 sheet: 0.55 (0.47), residues: 130 loop : -1.95 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 750 TYR 0.010 0.001 TYR B 636 PHE 0.017 0.001 PHE A 761 TRP 0.010 0.001 TRP B 635 HIS 0.008 0.001 HIS B1018 Details of bonding type rmsd covalent geometry : bond 0.00316 (14098) covalent geometry : angle 0.60603 (19144) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.28818 ( 12) hydrogen bonds : bond 0.04899 ( 678) hydrogen bonds : angle 4.21304 ( 1992) link_BETA1-4 : bond 0.00397 ( 4) link_BETA1-4 : angle 3.98735 ( 12) link_NAG-ASN : bond 0.00237 ( 4) link_NAG-ASN : angle 4.89261 ( 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 229 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.8617 (m-30) cc_final: 0.8297 (m-30) REVERT: A 509 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 536 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: A 543 GLN cc_start: 0.8268 (tt0) cc_final: 0.8012 (tm-30) REVERT: A 583 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8779 (mmt) REVERT: A 691 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7249 (tpp80) REVERT: A 732 GLU cc_start: 0.8405 (pt0) cc_final: 0.8137 (mt-10) REVERT: A 747 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: A 770 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8611 (tt) REVERT: A 783 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8537 (pp) REVERT: A 909 GLU cc_start: 0.6709 (tt0) cc_final: 0.6504 (tt0) REVERT: A 1016 ARG cc_start: 0.5742 (mtt180) cc_final: 0.5530 (mtt180) REVERT: B 315 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8049 (pp) REVERT: B 434 ILE cc_start: 0.7984 (mt) cc_final: 0.7780 (mp) REVERT: B 443 ASP cc_start: 0.8579 (m-30) cc_final: 0.8263 (m-30) REVERT: B 509 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8275 (mm) REVERT: B 536 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8421 (m-30) REVERT: B 543 GLN cc_start: 0.8264 (tt0) cc_final: 0.8001 (tm-30) REVERT: B 583 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8784 (mmt) REVERT: B 691 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7226 (tpp80) REVERT: B 732 GLU cc_start: 0.8393 (pt0) cc_final: 0.8125 (mt-10) REVERT: B 747 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: B 770 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8614 (tt) REVERT: B 783 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8505 (pp) REVERT: B 909 GLU cc_start: 0.6757 (tt0) cc_final: 0.6531 (tt0) REVERT: B 1016 ARG cc_start: 0.5731 (mtt180) cc_final: 0.5519 (mtt180) outliers start: 54 outliers final: 18 residues processed: 203 average time/residue: 0.6139 time to fit residues: 136.2142 Evaluate side-chains 190 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU 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 699 ASN 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 95 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 315 LEU 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 699 ASN 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: 2.9990 chunk 30 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 0.0970 chunk 167 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.150274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108434 restraints weight = 16456.852| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.18 r_work: 0.2882 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14112 Z= 0.100 Angle : 0.570 14.598 19180 Z= 0.275 Chirality : 0.041 0.197 2236 Planarity : 0.004 0.061 2392 Dihedral : 5.509 82.819 2076 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.62 % Allowed : 12.82 % Favored : 83.56 % 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: -0.55 (0.20), residues: 1770 helix: 0.53 (0.17), residues: 950 sheet: 0.70 (0.47), residues: 130 loop : -1.84 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 872 TYR 0.008 0.001 TYR B 427 PHE 0.011 0.001 PHE B 428 TRP 0.010 0.001 TRP A 661 HIS 0.012 0.001 HIS B1018 Details of bonding type rmsd covalent geometry : bond 0.00209 (14098) covalent geometry : angle 0.55123 (19144) SS BOND : bond 0.00241 ( 6) SS BOND : angle 1.02175 ( 12) hydrogen bonds : bond 0.03769 ( 678) hydrogen bonds : angle 3.86577 ( 1992) link_BETA1-4 : bond 0.00455 ( 4) link_BETA1-4 : angle 3.43815 ( 12) link_NAG-ASN : bond 0.00247 ( 4) link_NAG-ASN : angle 4.62525 ( 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 251 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.8095 (mt) cc_final: 0.7821 (mp) REVERT: A 443 ASP cc_start: 0.8658 (m-30) cc_final: 0.8353 (m-30) REVERT: A 536 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: A 543 GLN cc_start: 0.8412 (tt0) cc_final: 0.8137 (tm-30) REVERT: A 547 HIS cc_start: 0.7957 (m90) cc_final: 0.7498 (m-70) REVERT: A 583 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8821 (mmt) REVERT: A 691 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7235 (tpp80) REVERT: A 699 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8698 (t0) REVERT: A 743 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7975 (mm-40) REVERT: A 747 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: A 770 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8607 (tt) REVERT: A 783 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8241 (pp) REVERT: A 845 HIS cc_start: 0.7053 (m170) cc_final: 0.6814 (m170) REVERT: A 1016 ARG cc_start: 0.5931 (mtt180) cc_final: 0.5655 (mtt180) REVERT: A 1060 VAL cc_start: 0.8482 (t) cc_final: 0.8208 (t) REVERT: A 1077 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: B 315 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8077 (pp) REVERT: B 434 ILE cc_start: 0.8086 (mt) cc_final: 0.7882 (mp) REVERT: B 443 ASP cc_start: 0.8658 (m-30) cc_final: 0.8351 (m-30) REVERT: B 536 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: B 543 GLN cc_start: 0.8396 (tt0) cc_final: 0.8119 (tm-30) REVERT: B 547 HIS cc_start: 0.7952 (m90) cc_final: 0.7504 (m-70) REVERT: B 583 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8824 (mmt) REVERT: B 691 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7223 (tpp80) REVERT: B 699 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8671 (t0) REVERT: B 732 GLU cc_start: 0.8468 (pt0) cc_final: 0.8231 (mt-10) REVERT: B 743 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7987 (mm-40) REVERT: B 747 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: B 770 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8622 (tt) REVERT: B 783 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8225 (pp) REVERT: B 845 HIS cc_start: 0.7060 (m170) cc_final: 0.6813 (m170) REVERT: B 1016 ARG cc_start: 0.5911 (mtt180) cc_final: 0.5638 (mtt180) REVERT: B 1060 VAL cc_start: 0.8474 (t) cc_final: 0.8196 (t) REVERT: B 1077 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7396 (mt-10) outliers start: 53 outliers final: 12 residues processed: 230 average time/residue: 0.5694 time to fit residues: 144.3891 Evaluate side-chains 201 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 522 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 691 ARG Chi-restraints excluded: chain A residue 699 ASN 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 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 522 SER 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 699 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 HIS B 94 ASN B1018 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105055 restraints weight = 16516.957| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.13 r_work: 0.2931 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3185 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= 0.128 Angle : 0.603 15.637 19180 Z= 0.289 Chirality : 0.042 0.184 2236 Planarity : 0.004 0.059 2392 Dihedral : 5.300 98.339 2076 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.27 % Allowed : 12.76 % Favored : 83.97 % 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: -0.27 (0.20), residues: 1770 helix: 0.80 (0.17), residues: 948 sheet: 0.72 (0.47), residues: 130 loop : -1.77 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 750 TYR 0.011 0.001 TYR B 636 PHE 0.014 0.001 PHE B 761 TRP 0.009 0.001 TRP A 661 HIS 0.011 0.001 HIS A1018 Details of bonding type rmsd covalent geometry : bond 0.00304 (14098) covalent geometry : angle 0.58548 (19144) SS BOND : bond 0.00303 ( 6) SS BOND : angle 1.24239 ( 12) hydrogen bonds : bond 0.04047 ( 678) hydrogen bonds : angle 3.88522 ( 1992) link_BETA1-4 : bond 0.00461 ( 4) link_BETA1-4 : angle 3.11199 ( 12) link_NAG-ASN : bond 0.00164 ( 4) link_NAG-ASN : angle 4.85608 ( 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 219 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.8122 (mt) cc_final: 0.7843 (mp) REVERT: A 536 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: A 543 GLN cc_start: 0.8417 (tt0) cc_final: 0.8152 (tm-30) REVERT: A 547 HIS cc_start: 0.7958 (m90) cc_final: 0.7522 (m-70) REVERT: A 583 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8789 (mmt) REVERT: A 691 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7245 (tpp80) REVERT: A 743 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7888 (mm-40) REVERT: A 747 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: A 783 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8506 (pp) REVERT: A 845 HIS cc_start: 0.7017 (m170) cc_final: 0.6790 (m170) REVERT: A 1016 ARG cc_start: 0.5956 (mtt180) cc_final: 0.5681 (mtt180) REVERT: A 1060 VAL cc_start: 0.8530 (t) cc_final: 0.8321 (t) REVERT: A 1077 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: B 315 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8126 (pp) REVERT: B 434 ILE cc_start: 0.8137 (mt) cc_final: 0.7909 (mp) REVERT: B 443 ASP cc_start: 0.8652 (m-30) cc_final: 0.8301 (m-30) REVERT: B 536 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: B 543 GLN cc_start: 0.8403 (tt0) cc_final: 0.8138 (tm-30) REVERT: B 547 HIS cc_start: 0.7961 (m90) cc_final: 0.7531 (m-70) REVERT: B 583 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8790 (mmt) REVERT: B 691 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7246 (tpp80) REVERT: B 732 GLU cc_start: 0.8446 (pt0) cc_final: 0.8237 (mt-10) REVERT: B 743 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7883 (mm-40) REVERT: B 747 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: B 783 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8500 (pp) REVERT: B 845 HIS cc_start: 0.7040 (m170) cc_final: 0.6829 (m170) REVERT: B 1016 ARG cc_start: 0.5937 (mtt180) cc_final: 0.5668 (mtt180) REVERT: B 1060 VAL cc_start: 0.8526 (t) cc_final: 0.8315 (t) REVERT: B 1077 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7434 (mt-10) outliers start: 48 outliers final: 15 residues processed: 200 average time/residue: 0.6077 time to fit residues: 133.1777 Evaluate side-chains 190 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 439 ASN A1018 HIS B 94 ASN B 236 GLN B 439 ASN B 789 ASN B1018 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102008 restraints weight = 16539.828| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.12 r_work: 0.2884 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14112 Z= 0.189 Angle : 0.659 16.973 19180 Z= 0.317 Chirality : 0.045 0.183 2236 Planarity : 0.005 0.058 2392 Dihedral : 5.249 87.863 2076 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.16 % Allowed : 12.07 % 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: -0.34 (0.19), residues: 1770 helix: 0.77 (0.17), residues: 940 sheet: 0.89 (0.47), residues: 128 loop : -1.84 (0.20), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 750 TYR 0.012 0.002 TYR A 636 PHE 0.021 0.002 PHE B 834 TRP 0.010 0.002 TRP B 380 HIS 0.010 0.001 HIS A1018 Details of bonding type rmsd covalent geometry : bond 0.00467 (14098) covalent geometry : angle 0.64101 (19144) SS BOND : bond 0.00693 ( 6) SS BOND : angle 2.07556 ( 12) hydrogen bonds : bond 0.04834 ( 678) hydrogen bonds : angle 4.09277 ( 1992) link_BETA1-4 : bond 0.00456 ( 4) link_BETA1-4 : angle 2.75081 ( 12) link_NAG-ASN : bond 0.00239 ( 4) link_NAG-ASN : angle 5.25085 ( 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 239 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.8652 (m-30) cc_final: 0.8405 (m-30) REVERT: A 536 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8440 (m-30) REVERT: A 543 GLN cc_start: 0.8449 (tt0) cc_final: 0.8186 (tm-30) REVERT: A 583 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8776 (mmt) REVERT: A 691 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7415 (tpp80) REVERT: A 783 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8859 (pp) REVERT: A 845 HIS cc_start: 0.7045 (m170) cc_final: 0.6832 (m170) REVERT: A 1017 MET cc_start: 0.8310 (mmm) cc_final: 0.7452 (tpp) REVERT: A 1048 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7905 (ttm-80) REVERT: A 1060 VAL cc_start: 0.8615 (t) cc_final: 0.8397 (t) REVERT: B 536 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8450 (m-30) REVERT: B 543 GLN cc_start: 0.8452 (tt0) cc_final: 0.8164 (tm-30) REVERT: B 583 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8775 (mmt) REVERT: B 691 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7404 (tpp80) REVERT: B 783 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8857 (pp) REVERT: B 1017 MET cc_start: 0.8291 (mmm) cc_final: 0.7457 (tpp) REVERT: B 1048 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7886 (ttm-80) REVERT: B 1060 VAL cc_start: 0.8609 (t) cc_final: 0.8389 (t) REVERT: B 1077 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7392 (mt-10) outliers start: 61 outliers final: 23 residues processed: 213 average time/residue: 0.5802 time to fit residues: 135.5684 Evaluate side-chains 202 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 783 LEU Chi-restraints excluded: chain A residue 808 TRP 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 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 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 1033 ASP Chi-restraints excluded: chain B residue 1048 ARG 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: 0.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 699 ASN A1018 HIS B 94 ASN B 236 GLN B 699 ASN B1018 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.103639 restraints weight = 16497.626| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.22 r_work: 0.2914 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14112 Z= 0.108 Angle : 0.585 16.339 19180 Z= 0.281 Chirality : 0.042 0.188 2236 Planarity : 0.004 0.061 2392 Dihedral : 5.400 94.126 2076 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.00 % Allowed : 13.37 % 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: 0.08 (0.20), residues: 1770 helix: 1.13 (0.17), residues: 948 sheet: 0.85 (0.47), residues: 130 loop : -1.67 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 750 TYR 0.009 0.001 TYR B 636 PHE 0.011 0.001 PHE B 541 TRP 0.011 0.001 TRP B 850 HIS 0.008 0.001 HIS B1018 Details of bonding type rmsd covalent geometry : bond 0.00236 (14098) covalent geometry : angle 0.56811 (19144) SS BOND : bond 0.00333 ( 6) SS BOND : angle 1.81476 ( 12) hydrogen bonds : bond 0.03804 ( 678) hydrogen bonds : angle 3.82824 ( 1992) link_BETA1-4 : bond 0.00483 ( 4) link_BETA1-4 : angle 2.94369 ( 12) link_NAG-ASN : bond 0.00184 ( 4) link_NAG-ASN : angle 4.53210 ( 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 221 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8191 (pp) REVERT: A 435 MET cc_start: 0.8765 (mmt) cc_final: 0.8342 (mmt) REVERT: A 443 ASP cc_start: 0.8617 (m-30) cc_final: 0.8347 (m-30) REVERT: A 536 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: A 543 GLN cc_start: 0.8415 (tt0) cc_final: 0.8144 (tm-30) REVERT: A 583 MET cc_start: 0.8974 (tpp) cc_final: 0.8752 (mmt) REVERT: A 691 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7221 (tpp80) REVERT: A 783 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8574 (pp) REVERT: A 840 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7791 (mpt90) REVERT: A 845 HIS cc_start: 0.7061 (m170) cc_final: 0.6860 (m170) REVERT: A 1077 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: B 315 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8197 (pp) REVERT: B 434 ILE cc_start: 0.8208 (mt) cc_final: 0.7961 (mp) REVERT: B 536 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: B 543 GLN cc_start: 0.8414 (tt0) cc_final: 0.8146 (tm-30) REVERT: B 583 MET cc_start: 0.8980 (tpp) cc_final: 0.8752 (mmt) REVERT: B 691 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7217 (tpp80) REVERT: B 783 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8564 (pp) REVERT: B 840 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7718 (mpt90) REVERT: B 1060 VAL cc_start: 0.8565 (t) cc_final: 0.8363 (t) REVERT: B 1077 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7407 (mt-10) outliers start: 44 outliers final: 13 residues processed: 206 average time/residue: 0.5724 time to fit residues: 129.9431 Evaluate side-chains 198 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 480 VAL Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 783 LEU 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 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 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 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: 7.9990 chunk 157 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 699 ASN A1018 HIS B 236 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 = 0.3668 r_free = 0.3668 target = 0.147597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104738 restraints weight = 16413.938| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.15 r_work: 0.2952 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14112 Z= 0.116 Angle : 0.592 15.945 19180 Z= 0.285 Chirality : 0.042 0.185 2236 Planarity : 0.004 0.061 2392 Dihedral : 5.542 114.221 2076 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.93 % Allowed : 14.12 % 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: 0.23 (0.20), residues: 1770 helix: 1.26 (0.17), residues: 962 sheet: 1.16 (0.47), residues: 128 loop : -1.73 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 483 TYR 0.010 0.001 TYR B 636 PHE 0.011 0.001 PHE A 541 TRP 0.011 0.001 TRP B 850 HIS 0.009 0.001 HIS A1018 Details of bonding type rmsd covalent geometry : bond 0.00267 (14098) covalent geometry : angle 0.57544 (19144) SS BOND : bond 0.00329 ( 6) SS BOND : angle 1.67081 ( 12) hydrogen bonds : bond 0.03802 ( 678) hydrogen bonds : angle 3.79581 ( 1992) link_BETA1-4 : bond 0.00439 ( 4) link_BETA1-4 : angle 2.86733 ( 12) link_NAG-ASN : bond 0.00144 ( 4) link_NAG-ASN : angle 4.50732 ( 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 221 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8213 (pp) REVERT: A 536 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: A 543 GLN cc_start: 0.8427 (tt0) cc_final: 0.8154 (tm-30) REVERT: A 583 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8775 (mmt) REVERT: A 691 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7174 (tpp80) REVERT: A 783 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8589 (pp) REVERT: A 840 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7810 (mpt90) REVERT: A 845 HIS cc_start: 0.7053 (m170) cc_final: 0.6835 (m170) REVERT: A 1048 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7946 (ttm-80) REVERT: B 315 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8227 (pp) REVERT: B 434 ILE cc_start: 0.8205 (mt) cc_final: 0.7956 (mp) REVERT: B 536 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: B 543 GLN cc_start: 0.8412 (tt0) cc_final: 0.8139 (tm-30) REVERT: B 583 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8777 (mmt) REVERT: B 691 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7179 (tpp80) REVERT: B 783 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8584 (pp) REVERT: B 840 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7737 (mpt90) REVERT: B 1077 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7390 (mt-10) outliers start: 43 outliers final: 12 residues processed: 203 average time/residue: 0.5835 time to fit residues: 130.2041 Evaluate side-chains 192 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 783 LEU Chi-restraints excluded: chain A residue 840 ARG Chi-restraints excluded: chain A residue 1048 ARG 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 770 LEU Chi-restraints excluded: chain B residue 783 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 88 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 365 GLN A 699 ASN A1018 HIS B 236 GLN B 365 GLN B1018 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103346 restraints weight = 16570.465| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.16 r_work: 0.2955 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14112 Z= 0.130 Angle : 0.610 15.775 19180 Z= 0.294 Chirality : 0.043 0.208 2236 Planarity : 0.004 0.060 2392 Dihedral : 4.954 97.225 2074 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.66 % Allowed : 15.01 % 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: 0.29 (0.20), residues: 1770 helix: 1.32 (0.17), residues: 964 sheet: 1.13 (0.47), residues: 128 loop : -1.71 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 483 TYR 0.011 0.001 TYR B 636 PHE 0.012 0.001 PHE B 761 TRP 0.013 0.001 TRP B 850 HIS 0.008 0.001 HIS A1018 Details of bonding type rmsd covalent geometry : bond 0.00310 (14098) covalent geometry : angle 0.59387 (19144) SS BOND : bond 0.00360 ( 6) SS BOND : angle 1.71687 ( 12) hydrogen bonds : bond 0.03932 ( 678) hydrogen bonds : angle 3.79798 ( 1992) link_BETA1-4 : bond 0.00495 ( 4) link_BETA1-4 : angle 2.78639 ( 12) link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 4.54946 ( 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 208 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8239 (pp) REVERT: A 536 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: A 543 GLN cc_start: 0.8436 (tt0) cc_final: 0.8164 (tm-30) REVERT: A 583 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8757 (mmt) REVERT: A 691 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7171 (tpp80) REVERT: A 783 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8654 (pp) REVERT: A 840 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7788 (mpt90) REVERT: A 845 HIS cc_start: 0.7044 (m170) cc_final: 0.6827 (m170) REVERT: A 1048 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7970 (ttm-80) REVERT: A 1060 VAL cc_start: 0.8552 (t) cc_final: 0.8308 (t) REVERT: B 315 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8229 (pp) REVERT: B 434 ILE cc_start: 0.8227 (mt) cc_final: 0.7977 (mp) REVERT: B 536 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8431 (m-30) REVERT: B 543 GLN cc_start: 0.8420 (tt0) cc_final: 0.8147 (tm-30) REVERT: B 583 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8758 (mmt) REVERT: B 691 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7210 (tpp80) REVERT: B 783 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8651 (pp) REVERT: B 840 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7722 (mpt90) outliers start: 39 outliers final: 10 residues processed: 192 average time/residue: 0.6058 time to fit residues: 127.7091 Evaluate side-chains 188 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 696 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 840 ARG Chi-restraints excluded: chain A residue 1048 ARG 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 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 840 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 77 optimal weight: 0.0060 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 152 optimal weight: 0.3980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A1018 HIS B 236 GLN B 699 ASN B1018 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106006 restraints weight = 16473.704| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.16 r_work: 0.2999 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 14112 Z= 0.104 Angle : 0.584 15.119 19180 Z= 0.282 Chirality : 0.041 0.190 2236 Planarity : 0.004 0.062 2392 Dihedral : 4.319 20.190 2072 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.91 % Allowed : 16.03 % 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: 0.48 (0.20), residues: 1770 helix: 1.52 (0.17), residues: 962 sheet: 0.95 (0.47), residues: 130 loop : -1.65 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 750 TYR 0.009 0.001 TYR B 636 PHE 0.010 0.001 PHE A 428 TRP 0.018 0.001 TRP B 850 HIS 0.010 0.001 HIS B1018 Details of bonding type rmsd covalent geometry : bond 0.00235 (14098) covalent geometry : angle 0.56946 (19144) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.45784 ( 12) hydrogen bonds : bond 0.03419 ( 678) hydrogen bonds : angle 3.65134 ( 1992) link_BETA1-4 : bond 0.00496 ( 4) link_BETA1-4 : angle 2.90915 ( 12) link_NAG-ASN : bond 0.00170 ( 4) link_NAG-ASN : angle 4.19465 ( 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 213 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8204 (pp) REVERT: A 434 ILE cc_start: 0.8152 (mt) cc_final: 0.7860 (mp) REVERT: A 536 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: A 543 GLN cc_start: 0.8388 (tt0) cc_final: 0.8108 (tm-30) REVERT: A 547 HIS cc_start: 0.7890 (m90) cc_final: 0.7505 (m-70) REVERT: A 691 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7078 (tpp80) REVERT: A 783 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8432 (pp) REVERT: A 845 HIS cc_start: 0.7055 (m170) cc_final: 0.6843 (m170) REVERT: A 1060 VAL cc_start: 0.8561 (t) cc_final: 0.8324 (t) REVERT: B 315 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8147 (pp) REVERT: B 354 GLU cc_start: 0.7057 (pm20) cc_final: 0.6856 (pt0) REVERT: B 434 ILE cc_start: 0.8188 (mt) cc_final: 0.7962 (mp) REVERT: B 536 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8375 (m-30) REVERT: B 543 GLN cc_start: 0.8357 (tt0) cc_final: 0.8070 (tm-30) REVERT: B 547 HIS cc_start: 0.7890 (m90) cc_final: 0.7449 (m-70) REVERT: B 691 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7105 (tpp80) REVERT: B 783 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8449 (pp) REVERT: B 1060 VAL cc_start: 0.8501 (t) cc_final: 0.8273 (t) outliers start: 28 outliers final: 11 residues processed: 204 average time/residue: 0.5602 time to fit residues: 126.0201 Evaluate side-chains 198 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 480 VAL Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 1047 ASN 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 691 ARG Chi-restraints excluded: chain B residue 783 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A1018 HIS B 236 GLN B 853 HIS B1018 HIS ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103373 restraints weight = 16549.040| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.13 r_work: 0.2926 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3720 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= 0.163 Angle : 0.639 15.685 19180 Z= 0.306 Chirality : 0.044 0.192 2236 Planarity : 0.004 0.060 2392 Dihedral : 4.446 21.520 2072 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.98 % Allowed : 16.23 % Favored : 81.79 % 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: 0.34 (0.20), residues: 1770 helix: 1.41 (0.17), residues: 954 sheet: 1.08 (0.47), residues: 128 loop : -1.71 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1048 TYR 0.011 0.001 TYR B 636 PHE 0.014 0.001 PHE B 761 TRP 0.017 0.001 TRP B 850 HIS 0.009 0.001 HIS B1018 Details of bonding type rmsd covalent geometry : bond 0.00404 (14098) covalent geometry : angle 0.62385 (19144) SS BOND : bond 0.00385 ( 6) SS BOND : angle 1.83378 ( 12) hydrogen bonds : bond 0.04204 ( 678) hydrogen bonds : angle 3.85542 ( 1992) link_BETA1-4 : bond 0.00544 ( 4) link_BETA1-4 : angle 2.65251 ( 12) link_NAG-ASN : bond 0.00141 ( 4) link_NAG-ASN : angle 4.61787 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5494.40 seconds wall clock time: 94 minutes 3.91 seconds (5643.91 seconds total)