Starting phenix.real_space_refine on Thu Jul 31 18:41:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d99_30617/07_2025/7d99_30617.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d99_30617/07_2025/7d99_30617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2025/7d99_30617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2025/7d99_30617.map" model { file = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2025/7d99_30617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d99_30617/07_2025/7d99_30617.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: E, D, F, B Time building chain proxies: 14.95, per 1000 atoms: 1.08 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: 3.47 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.54 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: 4.79 Time building geometry restraints manager: 4.12 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: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.410 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.003 TRP A 339 HIS 0.012 0.002 HIS A 853 PHE 0.038 0.004 PHE B 761 TYR 0.021 0.003 TYR A 466 ARG 0.012 0.001 ARG A 674 Details of bonding type rmsd link_NAG-ASN : bond 0.01329 ( 4) link_NAG-ASN : angle 5.02570 ( 12) link_BETA1-4 : bond 0.00339 ( 4) link_BETA1-4 : angle 7.53535 ( 12) hydrogen bonds : bond 0.31965 ( 678) hydrogen bonds : angle 10.44993 ( 1992) SS BOND : bond 0.00303 ( 6) SS BOND : angle 2.92883 ( 12) covalent geometry : bond 0.00888 (14098) covalent geometry : angle 1.09486 (19144) *********************** 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 : 1.458 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: 1.4139 time to fit residues: 476.7197 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 : 1.599 ------------------------------------------------------------------------------- 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 150 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.148809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105427 restraints weight = 16318.109| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.14 r_work: 0.2962 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14112 Z= 0.137 Angle : 0.699 11.378 19180 Z= 0.348 Chirality : 0.045 0.226 2236 Planarity : 0.005 0.055 2392 Dihedral : 6.617 55.944 2076 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.73 % Allowed : 11.66 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.17), residues: 1770 helix: -1.60 (0.14), residues: 952 sheet: 0.33 (0.46), residues: 130 loop : -2.19 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 661 HIS 0.010 0.002 HIS A1018 PHE 0.018 0.002 PHE A 761 TYR 0.011 0.001 TYR B 427 ARG 0.006 0.001 ARG B 877 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 4.63362 ( 12) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 4.54144 ( 12) hydrogen bonds : bond 0.05768 ( 678) hydrogen bonds : angle 4.71070 ( 1992) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.43922 ( 12) covalent geometry : bond 0.00294 (14098) covalent geometry : angle 0.67923 (19144) *********************** 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 238 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.7609 (tt0) cc_final: 0.7290 (tp30) REVERT: A 358 GLN cc_start: 0.8271 (mt0) cc_final: 0.7964 (mt0) REVERT: A 435 MET cc_start: 0.8739 (mmt) cc_final: 0.8518 (mmt) REVERT: A 443 ASP cc_start: 0.8574 (m-30) cc_final: 0.8326 (m-30) REVERT: A 536 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8400 (m-30) REVERT: A 583 MET cc_start: 0.9028 (tpp) cc_final: 0.8819 (mmt) REVERT: A 747 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: A 774 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8113 (mpp) REVERT: A 1016 ARG cc_start: 0.5968 (mtt180) cc_final: 0.5666 (mtt180) REVERT: B 354 GLU cc_start: 0.7588 (tt0) cc_final: 0.7272 (tp30) REVERT: B 358 GLN cc_start: 0.8245 (mt0) cc_final: 0.7946 (mt0) REVERT: B 443 ASP cc_start: 0.8562 (m-30) cc_final: 0.8313 (m-30) REVERT: B 536 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8403 (m-30) REVERT: B 583 MET cc_start: 0.9040 (tpp) cc_final: 0.8826 (mmt) REVERT: B 747 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: B 774 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8136 (mpp) outliers start: 40 outliers final: 8 residues processed: 214 average time/residue: 1.2555 time to fit residues: 294.0544 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 : 1.440 ------------------------------------------------------------------------------- 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 140 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 HIS A 789 ASN B 776 HIS B 789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102646 restraints weight = 16506.638| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.13 r_work: 0.2930 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14112 Z= 0.184 Angle : 0.667 14.626 19180 Z= 0.326 Chirality : 0.045 0.193 2236 Planarity : 0.004 0.053 2392 Dihedral : 6.691 95.387 2076 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.62 % Allowed : 11.94 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.19), residues: 1770 helix: -0.28 (0.17), residues: 950 sheet: 0.53 (0.47), residues: 130 loop : -2.04 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 661 HIS 0.008 0.001 HIS A1018 PHE 0.022 0.002 PHE B 761 TYR 0.012 0.001 TYR A 636 ARG 0.006 0.001 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 4) link_NAG-ASN : angle 5.13013 ( 12) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 3.92473 ( 12) hydrogen bonds : bond 0.05386 ( 678) hydrogen bonds : angle 4.38425 ( 1992) SS BOND : bond 0.00406 ( 6) SS BOND : angle 1.60767 ( 12) covalent geometry : bond 0.00449 (14098) covalent geometry : angle 0.64681 (19144) *********************** 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 215 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.7510 (tt0) cc_final: 0.7197 (tp30) REVERT: A 358 GLN cc_start: 0.8279 (mt0) cc_final: 0.7907 (mt0) REVERT: A 443 ASP cc_start: 0.8667 (m-30) cc_final: 0.8372 (m-30) REVERT: A 536 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8421 (m-30) REVERT: A 543 GLN cc_start: 0.8414 (tt0) cc_final: 0.8168 (tm-30) REVERT: A 583 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8794 (mmt) REVERT: A 691 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7434 (tpp80) REVERT: A 747 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: A 770 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 774 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8235 (mpp) REVERT: A 783 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 909 GLU cc_start: 0.6911 (tt0) cc_final: 0.6707 (tt0) REVERT: B 354 GLU cc_start: 0.7520 (tt0) cc_final: 0.7192 (tp30) REVERT: B 358 GLN cc_start: 0.8263 (mt0) cc_final: 0.7818 (mt0) REVERT: B 443 ASP cc_start: 0.8668 (m-30) cc_final: 0.8373 (m-30) REVERT: B 536 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8403 (m-30) REVERT: B 543 GLN cc_start: 0.8421 (tt0) cc_final: 0.8175 (tm-30) REVERT: B 583 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8818 (mmt) REVERT: B 691 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7418 (tpp80) REVERT: B 699 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8724 (t0) REVERT: B 732 GLU cc_start: 0.8433 (pt0) cc_final: 0.8202 (mt-10) REVERT: B 747 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: B 770 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 774 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8234 (mpp) REVERT: B 783 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8805 (pp) REVERT: B 909 GLU cc_start: 0.6913 (tt0) cc_final: 0.6696 (tt0) REVERT: B 1016 ARG cc_start: 0.5897 (mtt180) cc_final: 0.5642 (mtt180) outliers start: 53 outliers final: 17 residues processed: 190 average time/residue: 1.2801 time to fit residues: 266.7314 Evaluate side-chains 187 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 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 774 MET 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 468 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 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 736 LEU Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 774 MET 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 102 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102761 restraints weight = 16420.387| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.07 r_work: 0.2853 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14112 Z= 0.172 Angle : 0.643 15.132 19180 Z= 0.313 Chirality : 0.044 0.185 2236 Planarity : 0.004 0.056 2392 Dihedral : 5.961 70.166 2076 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.02 % Allowed : 12.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1770 helix: 0.23 (0.17), residues: 946 sheet: 0.65 (0.47), residues: 130 loop : -1.87 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 661 HIS 0.011 0.001 HIS A1018 PHE 0.019 0.002 PHE B 761 TYR 0.011 0.001 TYR B 636 ARG 0.004 0.001 ARG B 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 5.28420 ( 12) link_BETA1-4 : bond 0.00384 ( 4) link_BETA1-4 : angle 3.34844 ( 12) hydrogen bonds : bond 0.04949 ( 678) hydrogen bonds : angle 4.17738 ( 1992) SS BOND : bond 0.00376 ( 6) SS BOND : angle 1.56142 ( 12) covalent geometry : bond 0.00419 (14098) covalent geometry : angle 0.62299 (19144) *********************** 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 232 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.7639 (tt0) cc_final: 0.7264 (tp30) REVERT: A 358 GLN cc_start: 0.8334 (mt0) cc_final: 0.7929 (mt0) REVERT: A 536 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8418 (m-30) REVERT: A 543 GLN cc_start: 0.8448 (tt0) cc_final: 0.8185 (tm-30) REVERT: A 583 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8773 (mmt) REVERT: A 691 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7410 (tpp80) REVERT: A 747 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: A 838 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7442 (pp30) REVERT: A 845 HIS cc_start: 0.7060 (m170) cc_final: 0.6803 (m170) REVERT: A 1060 VAL cc_start: 0.8520 (t) cc_final: 0.8307 (t) REVERT: B 354 GLU cc_start: 0.7615 (tt0) cc_final: 0.7227 (tp30) REVERT: B 358 GLN cc_start: 0.8327 (mt0) cc_final: 0.7921 (mt0) REVERT: B 536 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8428 (m-30) REVERT: B 543 GLN cc_start: 0.8450 (tt0) cc_final: 0.8186 (tm-30) REVERT: B 583 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8774 (mmt) REVERT: B 691 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7412 (tpp80) REVERT: B 699 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8786 (t0) REVERT: B 732 GLU cc_start: 0.8460 (pt0) cc_final: 0.8235 (mt-10) REVERT: B 747 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: B 783 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 838 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7423 (pp30) REVERT: B 1060 VAL cc_start: 0.8525 (t) cc_final: 0.8316 (t) outliers start: 59 outliers final: 20 residues processed: 210 average time/residue: 1.2136 time to fit residues: 280.0284 Evaluate side-chains 192 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 747 GLU 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 95 LEU 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 699 ASN Chi-restraints excluded: chain B residue 747 GLU 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 102 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN A1018 HIS B1018 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103334 restraints weight = 16545.731| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.12 r_work: 0.2885 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14112 Z= 0.118 Angle : 0.598 16.914 19180 Z= 0.288 Chirality : 0.042 0.188 2236 Planarity : 0.004 0.059 2392 Dihedral : 5.791 91.800 2076 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.96 % Allowed : 12.55 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1770 helix: 0.65 (0.17), residues: 958 sheet: 0.83 (0.47), residues: 130 loop : -1.74 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 661 HIS 0.010 0.001 HIS A1018 PHE 0.011 0.001 PHE B 541 TYR 0.010 0.001 TYR B 636 ARG 0.005 0.000 ARG B 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 4) link_NAG-ASN : angle 4.80514 ( 12) link_BETA1-4 : bond 0.00437 ( 4) link_BETA1-4 : angle 3.20468 ( 12) hydrogen bonds : bond 0.04129 ( 678) hydrogen bonds : angle 3.96331 ( 1992) SS BOND : bond 0.00311 ( 6) SS BOND : angle 1.19858 ( 12) covalent geometry : bond 0.00264 (14098) covalent geometry : angle 0.57972 (19144) *********************** 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 244 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8215 (pp) REVERT: A 354 GLU cc_start: 0.7654 (tt0) cc_final: 0.7231 (tp30) REVERT: A 358 GLN cc_start: 0.8203 (mt0) cc_final: 0.7558 (mt0) REVERT: A 536 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8405 (m-30) REVERT: A 543 GLN cc_start: 0.8395 (tt0) cc_final: 0.8148 (tm-30) REVERT: A 583 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8773 (mmt) REVERT: A 691 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7273 (tpp80) REVERT: A 770 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 838 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7468 (pp30) REVERT: A 845 HIS cc_start: 0.7080 (m170) cc_final: 0.6855 (m170) REVERT: B 315 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8228 (pp) REVERT: B 354 GLU cc_start: 0.7634 (tt0) cc_final: 0.7256 (tp30) REVERT: B 358 GLN cc_start: 0.8323 (mt0) cc_final: 0.7918 (mt0) REVERT: B 536 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: B 543 GLN cc_start: 0.8385 (tt0) cc_final: 0.8138 (tm-30) REVERT: B 583 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8769 (mmt) REVERT: B 691 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7284 (tpp80) REVERT: B 699 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8782 (t0) REVERT: B 743 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7967 (mm-40) REVERT: B 747 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 783 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 838 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7463 (pp30) REVERT: B 845 HIS cc_start: 0.7066 (m170) cc_final: 0.6806 (m170) outliers start: 58 outliers final: 15 residues processed: 219 average time/residue: 1.2354 time to fit residues: 297.3179 Evaluate side-chains 199 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 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 770 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 VAL 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 699 ASN Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 156 optimal weight: 0.7980 chunk 133 optimal weight: 0.1980 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 159 optimal weight: 0.0980 chunk 126 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 599 GLN A 699 ASN A1018 HIS B 94 ASN B 599 GLN B1018 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105134 restraints weight = 16613.955| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.17 r_work: 0.2871 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14112 Z= 0.100 Angle : 0.577 15.850 19180 Z= 0.275 Chirality : 0.041 0.182 2236 Planarity : 0.004 0.060 2392 Dihedral : 5.408 90.049 2076 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.62 % Allowed : 12.48 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1770 helix: 1.06 (0.17), residues: 946 sheet: 1.01 (0.48), residues: 130 loop : -1.66 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 850 HIS 0.012 0.001 HIS B1018 PHE 0.010 0.001 PHE B 541 TYR 0.008 0.001 TYR A 636 ARG 0.008 0.001 ARG B 750 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 4) link_NAG-ASN : angle 4.52221 ( 12) link_BETA1-4 : bond 0.00491 ( 4) link_BETA1-4 : angle 3.04916 ( 12) hydrogen bonds : bond 0.03612 ( 678) hydrogen bonds : angle 3.80555 ( 1992) SS BOND : bond 0.00285 ( 6) SS BOND : angle 1.08369 ( 12) covalent geometry : bond 0.00212 (14098) covalent geometry : angle 0.56032 (19144) *********************** 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 243 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8157 (pp) REVERT: A 434 ILE cc_start: 0.8120 (mt) cc_final: 0.7832 (mp) REVERT: A 443 ASP cc_start: 0.8578 (m-30) cc_final: 0.8295 (m-30) REVERT: A 536 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8431 (m-30) REVERT: A 543 GLN cc_start: 0.8378 (tt0) cc_final: 0.8112 (tm-30) REVERT: A 547 HIS cc_start: 0.7953 (m90) cc_final: 0.7485 (m-70) REVERT: A 583 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8769 (mmt) REVERT: A 691 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7122 (tpp80) REVERT: A 746 GLU cc_start: 0.8363 (tt0) cc_final: 0.8055 (tt0) REVERT: A 747 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: A 838 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7544 (pp30) REVERT: A 845 HIS cc_start: 0.7077 (m170) cc_final: 0.6831 (m170) REVERT: A 1016 ARG cc_start: 0.5957 (mtt180) cc_final: 0.5673 (mtt180) REVERT: A 1060 VAL cc_start: 0.8485 (t) cc_final: 0.8254 (t) REVERT: A 1077 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: B 315 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8133 (pp) REVERT: B 363 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: B 443 ASP cc_start: 0.8628 (m-30) cc_final: 0.8341 (m-30) REVERT: B 536 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: B 543 GLN cc_start: 0.8363 (tt0) cc_final: 0.8103 (tm-30) REVERT: B 547 HIS cc_start: 0.7916 (m90) cc_final: 0.7440 (m-70) REVERT: B 583 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8781 (mmt) REVERT: B 691 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7135 (tpp80) REVERT: B 699 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8814 (t0) REVERT: B 746 GLU cc_start: 0.8377 (tt0) cc_final: 0.8081 (tt0) REVERT: B 783 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 838 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7450 (pp30) REVERT: B 840 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7676 (mpt90) REVERT: B 1060 VAL cc_start: 0.8487 (t) cc_final: 0.8262 (t) REVERT: B 1077 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7490 (mt-10) outliers start: 53 outliers final: 14 residues processed: 222 average time/residue: 1.1554 time to fit residues: 283.3007 Evaluate side-chains 203 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 747 GLU 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 363 GLU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL 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 696 VAL Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 840 ARG Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 123 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 599 GLN A1018 HIS B 94 ASN B 599 GLN B1018 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.100545 restraints weight = 16621.497| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.14 r_work: 0.2780 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14112 Z= 0.227 Angle : 0.696 17.364 19180 Z= 0.336 Chirality : 0.046 0.180 2236 Planarity : 0.005 0.058 2392 Dihedral : 5.669 92.886 2076 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.82 % Allowed : 12.69 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1770 helix: 0.84 (0.17), residues: 944 sheet: 1.09 (0.48), residues: 128 loop : -1.80 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 380 HIS 0.009 0.001 HIS B1018 PHE 0.019 0.002 PHE B 761 TYR 0.012 0.002 TYR B 427 ARG 0.007 0.001 ARG A 750 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 5.27830 ( 12) link_BETA1-4 : bond 0.00451 ( 4) link_BETA1-4 : angle 2.57916 ( 12) hydrogen bonds : bond 0.05122 ( 678) hydrogen bonds : angle 4.13921 ( 1992) SS BOND : bond 0.00512 ( 6) SS BOND : angle 2.35908 ( 12) covalent geometry : bond 0.00570 (14098) covalent geometry : angle 0.67877 (19144) *********************** 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 234 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8439 (m-30) REVERT: A 543 GLN cc_start: 0.8457 (tt0) cc_final: 0.8190 (tm-30) REVERT: A 583 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8769 (mmt) REVERT: A 691 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7386 (tpp80) REVERT: A 743 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7841 (mm110) REVERT: A 746 GLU cc_start: 0.8285 (tt0) cc_final: 0.8064 (tt0) REVERT: A 838 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7408 (pp30) REVERT: A 840 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7858 (mpt90) REVERT: A 875 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7414 (tmm160) REVERT: A 1060 VAL cc_start: 0.8633 (t) cc_final: 0.8397 (t) REVERT: B 261 LEU cc_start: 0.8685 (tp) cc_final: 0.8453 (tp) REVERT: B 363 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: B 536 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: B 543 GLN cc_start: 0.8453 (tt0) cc_final: 0.8185 (tm-30) REVERT: B 583 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8765 (mmt) REVERT: B 691 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7401 (tpp80) REVERT: B 746 GLU cc_start: 0.8300 (tt0) cc_final: 0.7995 (tt0) REVERT: B 783 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8935 (pp) REVERT: B 838 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7410 (pp30) REVERT: B 840 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7926 (mpt90) REVERT: B 1060 VAL cc_start: 0.8623 (t) cc_final: 0.8385 (t) outliers start: 56 outliers final: 24 residues processed: 209 average time/residue: 1.2999 time to fit residues: 297.8696 Evaluate side-chains 208 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 840 ARG Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 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 838 GLN Chi-restraints excluded: chain B residue 840 ARG Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 166 optimal weight: 0.0050 chunk 148 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 699 ASN A1018 HIS B 94 ASN B 236 GLN B1018 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104714 restraints weight = 16475.740| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.17 r_work: 0.2944 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14112 Z= 0.102 Angle : 0.589 16.407 19180 Z= 0.283 Chirality : 0.041 0.185 2236 Planarity : 0.004 0.062 2392 Dihedral : 5.426 92.764 2076 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.52 % Allowed : 14.32 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1770 helix: 1.21 (0.17), residues: 950 sheet: 1.24 (0.48), residues: 128 loop : -1.66 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 850 HIS 0.010 0.001 HIS A1018 PHE 0.011 0.001 PHE B 541 TYR 0.009 0.001 TYR B 636 ARG 0.006 0.001 ARG B 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 4) link_NAG-ASN : angle 4.34684 ( 12) link_BETA1-4 : bond 0.00500 ( 4) link_BETA1-4 : angle 2.94149 ( 12) hydrogen bonds : bond 0.03677 ( 678) hydrogen bonds : angle 3.83503 ( 1992) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.93223 ( 12) covalent geometry : bond 0.00214 (14098) covalent geometry : angle 0.57261 (19144) *********************** 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 216 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8199 (pp) REVERT: A 434 ILE cc_start: 0.8176 (mt) cc_final: 0.7939 (mp) REVERT: A 443 ASP cc_start: 0.8682 (m-30) cc_final: 0.8441 (m-30) REVERT: A 536 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8439 (m-30) REVERT: A 543 GLN cc_start: 0.8388 (tt0) cc_final: 0.8117 (tm-30) REVERT: A 583 MET cc_start: 0.8965 (tpp) cc_final: 0.8582 (mmm) REVERT: A 691 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7164 (tpp80) REVERT: A 746 GLU cc_start: 0.8243 (tt0) cc_final: 0.7976 (tt0) REVERT: A 838 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7349 (pp30) REVERT: A 840 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7648 (mpt90) REVERT: A 845 HIS cc_start: 0.7058 (m170) cc_final: 0.6848 (m170) REVERT: A 1060 VAL cc_start: 0.8599 (t) cc_final: 0.8342 (t) REVERT: B 188 MET cc_start: 0.9190 (ptt) cc_final: 0.8988 (ptm) REVERT: B 261 LEU cc_start: 0.8590 (tp) cc_final: 0.8373 (tp) REVERT: B 315 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8198 (pp) REVERT: B 443 ASP cc_start: 0.8685 (m-30) cc_final: 0.8446 (m-30) REVERT: B 536 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: B 543 GLN cc_start: 0.8373 (tt0) cc_final: 0.8098 (tm-30) REVERT: B 583 MET cc_start: 0.8967 (tpp) cc_final: 0.8589 (mmm) REVERT: B 691 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7168 (tpp80) REVERT: B 746 GLU cc_start: 0.8245 (tt0) cc_final: 0.7900 (tt0) REVERT: B 783 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8543 (pp) REVERT: B 838 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7372 (pp30) REVERT: B 840 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7707 (mpt90) REVERT: B 1060 VAL cc_start: 0.8589 (t) cc_final: 0.8335 (t) outliers start: 37 outliers final: 16 residues processed: 203 average time/residue: 1.1672 time to fit residues: 261.4091 Evaluate side-chains 200 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 570 LEU 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 838 GLN Chi-restraints excluded: chain A residue 840 ARG Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain B residue 179 VAL 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 570 LEU 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 838 GLN Chi-restraints excluded: chain B residue 840 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 84 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 30 optimal weight: 0.0470 chunk 139 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 66 optimal weight: 0.0170 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN A1018 HIS B 236 GLN B 365 GLN B1018 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104422 restraints weight = 16431.025| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.12 r_work: 0.2928 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3692 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= 0.114 Angle : 0.600 15.925 19180 Z= 0.287 Chirality : 0.042 0.195 2236 Planarity : 0.004 0.063 2392 Dihedral : 4.425 20.678 2072 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.25 % Allowed : 15.08 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1770 helix: 1.31 (0.17), residues: 962 sheet: 1.07 (0.48), residues: 132 loop : -1.66 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 661 HIS 0.010 0.001 HIS B1018 PHE 0.010 0.001 PHE B 541 TYR 0.010 0.001 TYR B 636 ARG 0.006 0.000 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 4) link_NAG-ASN : angle 4.41882 ( 12) link_BETA1-4 : bond 0.00479 ( 4) link_BETA1-4 : angle 2.79498 ( 12) hydrogen bonds : bond 0.03735 ( 678) hydrogen bonds : angle 3.77966 ( 1992) SS BOND : bond 0.00324 ( 6) SS BOND : angle 1.81492 ( 12) covalent geometry : bond 0.00269 (14098) covalent geometry : angle 0.58392 (19144) *********************** 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 218 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8199 (pp) REVERT: A 443 ASP cc_start: 0.8704 (m-30) cc_final: 0.8435 (m-30) REVERT: A 536 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: A 543 GLN cc_start: 0.8394 (tt0) cc_final: 0.8129 (tm-30) REVERT: A 583 MET cc_start: 0.8967 (tpp) cc_final: 0.8757 (mmt) REVERT: A 691 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7116 (tpp80) REVERT: A 746 GLU cc_start: 0.8229 (tt0) cc_final: 0.8001 (tt0) REVERT: A 845 HIS cc_start: 0.7103 (m170) cc_final: 0.6890 (m170) REVERT: A 1060 VAL cc_start: 0.8568 (t) cc_final: 0.8304 (t) REVERT: B 315 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8211 (pp) REVERT: B 443 ASP cc_start: 0.8708 (m-30) cc_final: 0.8443 (m-30) REVERT: B 536 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: B 543 GLN cc_start: 0.8381 (tt0) cc_final: 0.8107 (tm-30) REVERT: B 583 MET cc_start: 0.8969 (tpp) cc_final: 0.8758 (mmt) REVERT: B 691 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7117 (tpp80) REVERT: B 746 GLU cc_start: 0.8239 (tt0) cc_final: 0.8002 (tt0) REVERT: B 783 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8579 (pp) REVERT: B 1060 VAL cc_start: 0.8556 (t) cc_final: 0.8297 (t) outliers start: 33 outliers final: 14 residues processed: 209 average time/residue: 1.1726 time to fit residues: 270.2106 Evaluate side-chains 193 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 522 SER 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 1049 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 102 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 699 ASN A1018 HIS B 236 GLN B 599 GLN B1018 HIS ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104267 restraints weight = 16537.703| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.13 r_work: 0.2944 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14112 Z= 0.115 Angle : 0.603 15.463 19180 Z= 0.290 Chirality : 0.042 0.197 2236 Planarity : 0.004 0.064 2392 Dihedral : 4.409 20.738 2072 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.91 % Allowed : 15.83 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1770 helix: 1.41 (0.17), residues: 962 sheet: 1.10 (0.48), residues: 132 loop : -1.62 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 850 HIS 0.010 0.001 HIS A1018 PHE 0.010 0.001 PHE B 541 TYR 0.010 0.001 TYR B 636 ARG 0.006 0.000 ARG B 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 4) link_NAG-ASN : angle 4.35269 ( 12) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 2.82203 ( 12) hydrogen bonds : bond 0.03698 ( 678) hydrogen bonds : angle 3.76721 ( 1992) SS BOND : bond 0.00337 ( 6) SS BOND : angle 1.78649 ( 12) covalent geometry : bond 0.00273 (14098) covalent geometry : angle 0.58813 (19144) ********************** 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 : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 434 ILE cc_start: 0.8213 (mt) cc_final: 0.7968 (mp) REVERT: A 443 ASP cc_start: 0.8701 (m-30) cc_final: 0.8397 (m-30) REVERT: A 536 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: A 543 GLN cc_start: 0.8390 (tt0) cc_final: 0.8106 (tm-30) REVERT: A 547 HIS cc_start: 0.7896 (m90) cc_final: 0.7447 (m-70) REVERT: A 583 MET cc_start: 0.8962 (tpp) cc_final: 0.8750 (mmt) REVERT: A 691 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7143 (tpp80) REVERT: A 746 GLU cc_start: 0.8212 (tt0) cc_final: 0.7980 (tt0) REVERT: A 1060 VAL cc_start: 0.8598 (t) cc_final: 0.8348 (t) REVERT: B 315 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8214 (pp) REVERT: B 443 ASP cc_start: 0.8736 (m-30) cc_final: 0.8439 (m-30) REVERT: B 536 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: B 543 GLN cc_start: 0.8386 (tt0) cc_final: 0.8104 (tm-30) REVERT: B 547 HIS cc_start: 0.7877 (m90) cc_final: 0.7425 (m-70) REVERT: B 583 MET cc_start: 0.8964 (tpp) cc_final: 0.8758 (mmt) REVERT: B 691 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7101 (tpp80) REVERT: B 746 GLU cc_start: 0.8241 (tt0) cc_final: 0.8017 (tt0) REVERT: B 783 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8559 (pp) REVERT: B 1060 VAL cc_start: 0.8555 (t) cc_final: 0.8286 (t) outliers start: 28 outliers final: 15 residues processed: 206 average time/residue: 1.1412 time to fit residues: 261.4175 Evaluate side-chains 203 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 522 SER Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 808 TRP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN A 853 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103887 restraints weight = 16561.481| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.13 r_work: 0.2945 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3769 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= 0.139 Angle : 0.623 15.567 19180 Z= 0.298 Chirality : 0.043 0.189 2236 Planarity : 0.004 0.062 2392 Dihedral : 4.452 21.423 2072 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.84 % Allowed : 16.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1770 helix: 1.39 (0.17), residues: 958 sheet: 1.09 (0.48), residues: 132 loop : -1.64 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 850 HIS 0.009 0.001 HIS A1018 PHE 0.011 0.001 PHE A 541 TYR 0.011 0.001 TYR A 636 ARG 0.006 0.001 ARG B 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 4) link_NAG-ASN : angle 4.54024 ( 12) link_BETA1-4 : bond 0.00431 ( 4) link_BETA1-4 : angle 2.71990 ( 12) hydrogen bonds : bond 0.04040 ( 678) hydrogen bonds : angle 3.84229 ( 1992) SS BOND : bond 0.00358 ( 6) SS BOND : angle 1.86322 ( 12) covalent geometry : bond 0.00343 (14098) covalent geometry : angle 0.60751 (19144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12101.80 seconds wall clock time: 209 minutes 4.45 seconds (12544.45 seconds total)