Starting phenix.real_space_refine on Fri Mar 6 17:57:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rn4_4942/03_2026/6rn4_4942.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rn4_4942/03_2026/6rn4_4942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rn4_4942/03_2026/6rn4_4942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rn4_4942/03_2026/6rn4_4942.map" model { file = "/net/cci-nas-00/data/ceres_data/6rn4_4942/03_2026/6rn4_4942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rn4_4942/03_2026/6rn4_4942.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 126 5.16 5 C 20458 2.51 5 N 5926 2.21 5 O 6291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32833 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5340 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 5364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5364 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 656} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.85, per 1000 atoms: 0.24 Number of scatterers: 32833 At special positions: 0 Unit cell: (141.44, 183.04, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 32 15.00 O 6291 8.00 N 5926 7.00 C 20458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7672 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 32 sheets defined 64.4% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.630A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 4.272A pdb=" N GLY A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 342 through 361 removed outlier: 4.454A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.601A pdb=" N ILE A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 443 through 493 Processing helix chain 'A' and resid 494 through 524 removed outlier: 3.682A pdb=" N MET A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 561 through 570 removed outlier: 4.158A pdb=" N ARG A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 Processing helix chain 'A' and resid 610 through 623 Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.865A pdb=" N GLU A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.771A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 734 through 749 Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'A' and resid 814 through 835 Proline residue: A 828 - end of helix Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.737A pdb=" N TYR B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 164' Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.678A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.557A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.658A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 305' Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.632A pdb=" N TYR B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 Processing helix chain 'B' and resid 387 through 406 Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 443 through 493 Processing helix chain 'B' and resid 494 through 524 removed outlier: 3.968A pdb=" N MET B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.717A pdb=" N VAL B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 624 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.696A pdb=" N GLU B 636 " --> pdb=" O ASP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 647 Processing helix chain 'B' and resid 653 through 657 removed outlier: 3.919A pdb=" N TYR B 656 " --> pdb=" O TYR B 653 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 657 " --> pdb=" O VAL B 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 653 through 657' Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.617A pdb=" N GLU B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 removed outlier: 4.003A pdb=" N PHE B 687 " --> pdb=" O PRO B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 733 through 749 removed outlier: 3.837A pdb=" N MET B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 807 removed outlier: 3.713A pdb=" N LEU B 800 " --> pdb=" O SER B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 834 Proline residue: B 828 - end of helix removed outlier: 3.996A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.764A pdb=" N GLN C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.607A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 298 through 305 removed outlier: 4.635A pdb=" N ALA C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.897A pdb=" N ARG C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 323 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.601A pdb=" N THR C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 380 removed outlier: 3.831A pdb=" N ILE C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 443 through 493 Processing helix chain 'C' and resid 494 through 524 removed outlier: 3.947A pdb=" N MET C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Proline residue: C 507 - end of helix removed outlier: 3.549A pdb=" N MET C 524 " --> pdb=" O GLU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 542 removed outlier: 3.928A pdb=" N ILE C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 561 Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 573 through 590 removed outlier: 3.648A pdb=" N VAL C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 623 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 655 through 659 removed outlier: 3.794A pdb=" N GLU C 658 " --> pdb=" O GLY C 655 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 659 " --> pdb=" O TYR C 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 655 through 659' Processing helix chain 'C' and resid 661 through 669 removed outlier: 3.666A pdb=" N ALA C 665 " --> pdb=" O TYR C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 682 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.844A pdb=" N LEU C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 729 Processing helix chain 'C' and resid 733 through 749 removed outlier: 3.873A pdb=" N MET C 737 " --> pdb=" O ASP C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 788 Processing helix chain 'C' and resid 796 through 808 removed outlier: 3.655A pdb=" N LEU C 800 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 801 " --> pdb=" O ASP C 797 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 808 " --> pdb=" O SER C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 834 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 241 through 248 Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.200A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY D 285 " --> pdb=" O HIS D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.287A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.571A pdb=" N TYR D 319 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 342 through 361 removed outlier: 3.576A pdb=" N THR D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 387 through 407 removed outlier: 3.523A pdb=" N ILE D 391 " --> pdb=" O PRO D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 443 through 493 Processing helix chain 'D' and resid 494 through 524 removed outlier: 3.760A pdb=" N MET D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Proline residue: D 507 - end of helix Processing helix chain 'D' and resid 532 through 544 Processing helix chain 'D' and resid 552 through 561 Processing helix chain 'D' and resid 561 through 567 removed outlier: 3.716A pdb=" N HIS D 567 " --> pdb=" O GLU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 589 removed outlier: 3.670A pdb=" N VAL D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 624 Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 653 through 657 removed outlier: 3.819A pdb=" N TYR D 656 " --> pdb=" O TYR D 653 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU D 657 " --> pdb=" O VAL D 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 653 through 657' Processing helix chain 'D' and resid 661 through 669 removed outlier: 3.502A pdb=" N ALA D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.793A pdb=" N LYS D 681 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA D 682 " --> pdb=" O VAL D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 684 through 697 Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 734 through 749 Processing helix chain 'D' and resid 767 through 790 Processing helix chain 'D' and resid 796 through 806 Processing helix chain 'D' and resid 814 through 834 removed outlier: 3.774A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 211 through 225 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 241 through 248 removed outlier: 3.580A pdb=" N LEU E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 270 removed outlier: 3.659A pdb=" N GLU E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 Processing helix chain 'E' and resid 295 through 304 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 326 through 333 removed outlier: 5.574A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 332 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 362 removed outlier: 3.577A pdb=" N THR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 381 removed outlier: 3.617A pdb=" N ILE E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 410 through 430 Processing helix chain 'E' and resid 443 through 493 Processing helix chain 'E' and resid 495 through 524 Proline residue: E 507 - end of helix Processing helix chain 'E' and resid 532 through 545 removed outlier: 3.749A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 570 removed outlier: 3.771A pdb=" N ARG E 556 " --> pdb=" O MET E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.790A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 624 removed outlier: 3.607A pdb=" N LEU E 614 " --> pdb=" O GLY E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 647 Processing helix chain 'E' and resid 655 through 659 removed outlier: 3.639A pdb=" N GLY E 659 " --> pdb=" O TYR E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 668 Processing helix chain 'E' and resid 678 through 682 Processing helix chain 'E' and resid 685 through 696 removed outlier: 4.249A pdb=" N ILE E 689 " --> pdb=" O ASP E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 734 through 749 Processing helix chain 'E' and resid 750 through 755 removed outlier: 3.772A pdb=" N ASN E 755 " --> pdb=" O PRO E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 790 removed outlier: 3.950A pdb=" N GLU E 788 " --> pdb=" O LYS E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 807 removed outlier: 3.821A pdb=" N LEU E 800 " --> pdb=" O SER E 796 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS E 801 " --> pdb=" O ASP E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 834 removed outlier: 3.535A pdb=" N LYS E 818 " --> pdb=" O ALA E 814 " (cutoff:3.500A) Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.853A pdb=" N TYR F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 164' Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 211 through 225 Processing helix chain 'F' and resid 241 through 246 removed outlier: 3.859A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 270 Processing helix chain 'F' and resid 279 through 286 Processing helix chain 'F' and resid 295 through 304 Proline residue: F 301 - end of helix removed outlier: 3.680A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.937A pdb=" N ARG F 320 " --> pdb=" O LEU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 332 Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.700A pdb=" N THR F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 406 Processing helix chain 'F' and resid 410 through 430 Processing helix chain 'F' and resid 443 through 493 Processing helix chain 'F' and resid 494 through 524 removed outlier: 3.928A pdb=" N MET F 498 " --> pdb=" O ASP F 494 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER F 499 " --> pdb=" O LEU F 495 " (cutoff:3.500A) Proline residue: F 507 - end of helix Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 554 through 566 Processing helix chain 'F' and resid 573 through 590 removed outlier: 3.621A pdb=" N GLY F 590 " --> pdb=" O ARG F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 622 Processing helix chain 'F' and resid 635 through 638 removed outlier: 4.196A pdb=" N MET F 638 " --> pdb=" O SER F 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 635 through 638' Processing helix chain 'F' and resid 641 through 648 removed outlier: 3.559A pdb=" N ARG F 645 " --> pdb=" O HIS F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 669 Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.563A pdb=" N ALA F 682 " --> pdb=" O VAL F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 696 removed outlier: 3.606A pdb=" N PHE F 687 " --> pdb=" O HIS F 683 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 729 Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 750 through 755 Processing helix chain 'F' and resid 768 through 790 Processing helix chain 'F' and resid 796 through 808 Processing helix chain 'F' and resid 813 through 834 Proline residue: F 828 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 3.625A pdb=" N ILE A 166 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 239 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 603 removed outlier: 5.221A pdb=" N GLY A 599 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET A 716 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE A 601 " --> pdb=" O MET A 716 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.649A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 793 through 795 Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.998A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.373A pdb=" N GLN B 364 " --> pdb=" O VAL B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 630 through 631 removed outlier: 6.693A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 717 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLY B 599 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N MET B 716 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 601 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER B 718 " --> pdb=" O PHE B 601 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE B 603 " --> pdb=" O SER B 718 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AB2, first strand: chain 'B' and resid 792 through 795 Processing sheet with id=AB3, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.089A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 314 through 315 removed outlier: 7.865A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 364 through 365 removed outlier: 7.320A pdb=" N GLN C 364 " --> pdb=" O VAL C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 600 through 603 removed outlier: 5.640A pdb=" N PHE C 601 " --> pdb=" O MET C 716 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 698 through 699 removed outlier: 3.674A pdb=" N VAL C 707 " --> pdb=" O LEU C 699 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 793 through 795 removed outlier: 7.006A pdb=" N HIS C 794 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL C 848 " --> pdb=" O HIS C 794 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 165 through 167 removed outlier: 5.789A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 312 through 313 removed outlier: 3.518A pdb=" N VAL D 336 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 631 through 633 removed outlier: 7.611A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 676 " --> pdb=" O THR D 717 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU D 602 " --> pdb=" O VAL D 761 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 698 through 699 Processing sheet with id=AC4, first strand: chain 'D' and resid 792 through 795 removed outlier: 6.427A pdb=" N GLU D 792 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU D 846 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N VAL D 848 " --> pdb=" O HIS D 794 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 165 through 167 removed outlier: 5.977A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 312 through 315 removed outlier: 5.908A pdb=" N LEU E 204 " --> pdb=" O THR E 314 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 364 through 365 removed outlier: 7.791A pdb=" N GLN E 364 " --> pdb=" O VAL E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.131A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL E 761 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU E 602 " --> pdb=" O VAL E 761 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 792 through 795 removed outlier: 6.457A pdb=" N GLU E 792 " --> pdb=" O ILE E 844 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU E 846 " --> pdb=" O GLU E 792 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N HIS E 794 " --> pdb=" O LEU E 846 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL E 848 " --> pdb=" O HIS E 794 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.864A pdb=" N ARG F 236 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE F 276 " --> pdb=" O ARG F 236 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU F 238 " --> pdb=" O PHE F 276 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 312 through 315 removed outlier: 8.023A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 203 " --> pdb=" O GLN F 334 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.547A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 630 through 633 removed outlier: 3.715A pdb=" N LEU F 675 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE F 632 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP F 677 " --> pdb=" O ILE F 632 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE F 601 " --> pdb=" O MET F 716 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER F 718 " --> pdb=" O PHE F 601 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE F 603 " --> pdb=" O SER F 718 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 792 through 795 removed outlier: 6.920A pdb=" N GLU F 792 " --> pdb=" O ILE F 844 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU F 846 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 843 " --> pdb=" O HIS F 858 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS F 858 " --> pdb=" O VAL F 843 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1838 hydrogen bonds defined for protein. 5427 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: 6.67 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 5973 1.32 - 1.48: 12611 1.48 - 1.64: 14471 1.64 - 1.80: 183 1.80 - 1.96: 47 Bond restraints: 33285 Sorted by residual: bond pdb=" C GLY B 253 " pdb=" N GLU B 254 " ideal model delta sigma weight residual 1.331 1.265 0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.46e-02 4.69e+03 1.60e+01 bond pdb=" C LEU D 177 " pdb=" N ASP D 178 " ideal model delta sigma weight residual 1.331 1.271 0.061 1.63e-02 3.76e+03 1.39e+01 bond pdb=" CB GLU E 613 " pdb=" CG GLU E 613 " ideal model delta sigma weight residual 1.520 1.411 0.109 3.00e-02 1.11e+03 1.33e+01 bond pdb=" CB ASP D 388 " pdb=" CG ASP D 388 " ideal model delta sigma weight residual 1.516 1.430 0.086 2.50e-02 1.60e+03 1.20e+01 ... (remaining 33280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.60: 44845 7.60 - 15.20: 78 15.20 - 22.79: 5 22.79 - 30.39: 0 30.39 - 37.99: 1 Bond angle restraints: 44929 Sorted by residual: angle pdb=" O1B AGS F1001 " pdb=" PB AGS F1001 " pdb=" O2B AGS F1001 " ideal model delta sigma weight residual 112.09 74.10 37.99 4.09e+00 5.99e-02 8.64e+01 angle pdb=" C SER F 407 " pdb=" N PRO F 409 " pdb=" CA PRO F 409 " ideal model delta sigma weight residual 127.00 148.13 -21.13 2.40e+00 1.74e-01 7.75e+01 angle pdb=" N VAL C 686 " pdb=" CA VAL C 686 " pdb=" C VAL C 686 " ideal model delta sigma weight residual 113.22 103.26 9.96 1.23e+00 6.61e-01 6.56e+01 angle pdb=" C SER F 407 " pdb=" N PRO F 409 " pdb=" CD PRO F 409 " ideal model delta sigma weight residual 120.60 103.04 17.56 2.20e+00 2.07e-01 6.37e+01 angle pdb=" N LEU F 444 " pdb=" CA LEU F 444 " pdb=" C LEU F 444 " ideal model delta sigma weight residual 113.50 106.14 7.36 1.23e+00 6.61e-01 3.58e+01 ... (remaining 44924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.66: 20139 27.66 - 55.31: 463 55.31 - 82.97: 36 82.97 - 110.62: 0 110.62 - 138.28: 2 Dihedral angle restraints: 20640 sinusoidal: 8765 harmonic: 11875 Sorted by residual: dihedral pdb=" CA GLY F 608 " pdb=" C GLY F 608 " pdb=" N VAL F 609 " pdb=" CA VAL F 609 " ideal model delta harmonic sigma weight residual -180.00 -131.68 -48.32 0 5.00e+00 4.00e-02 9.34e+01 dihedral pdb=" CA TYR A 656 " pdb=" C TYR A 656 " pdb=" N GLU A 657 " pdb=" CA GLU A 657 " ideal model delta harmonic sigma weight residual -180.00 -145.65 -34.35 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA VAL B 548 " pdb=" C VAL B 548 " pdb=" N SER B 549 " pdb=" CA SER B 549 " ideal model delta harmonic sigma weight residual 180.00 -146.37 -33.63 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 20637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4288 0.085 - 0.171: 749 0.171 - 0.256: 45 0.256 - 0.342: 5 0.342 - 0.427: 1 Chirality restraints: 5088 Sorted by residual: chirality pdb=" PA AGS D1002 " pdb=" O2A AGS D1002 " pdb=" O3A AGS D1002 " pdb=" O5' AGS D1002 " both_signs ideal model delta sigma weight residual True 3.18 -2.75 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CB VAL B 679 " pdb=" CA VAL B 679 " pdb=" CG1 VAL B 679 " pdb=" CG2 VAL B 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" PA AGS C1001 " pdb=" O2A AGS C1001 " pdb=" O3A AGS C1001 " pdb=" O5' AGS C1001 " both_signs ideal model delta sigma weight residual True 3.18 -2.89 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5085 not shown) Planarity restraints: 5869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 661 " -0.036 2.00e-02 2.50e+03 2.79e-02 1.56e+01 pdb=" CG TYR E 661 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR E 661 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 661 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 661 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 661 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 661 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 661 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 643 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C VAL C 643 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL C 643 " -0.023 2.00e-02 2.50e+03 pdb=" N SER C 644 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS E 683 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO E 684 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO E 684 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 684 " 0.045 5.00e-02 4.00e+02 ... (remaining 5866 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1259 2.69 - 3.24: 32264 3.24 - 3.79: 54447 3.79 - 4.35: 67768 4.35 - 4.90: 109390 Nonbonded interactions: 265128 Sorted by model distance: nonbonded pdb=" O GLY F 608 " pdb=" O1B AGS F1001 " model vdw 2.132 2.432 nonbonded pdb=" O1B AGS E1001 " pdb=" O2A AGS E1001 " model vdw 2.173 3.040 nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.223 3.040 nonbonded pdb=" O1B AGS C1001 " pdb=" O2G AGS C1001 " model vdw 2.225 3.040 nonbonded pdb=" O2A AGS B1001 " pdb=" O2B AGS B1001 " model vdw 2.226 3.040 ... (remaining 265123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 1001)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 1001)) selection = (chain 'D' and (resid 159 through 543 or resid 553 through 1001)) selection = (chain 'E' and (resid 159 through 543 or resid 553 through 1001)) selection = (chain 'F' and (resid 159 through 287 or resid 293 through 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.520 Find NCS groups from input model: 0.750 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.012 0.185 33304 Z= 0.519 Angle : 1.245 37.988 44929 Z= 0.660 Chirality : 0.062 0.427 5088 Planarity : 0.008 0.084 5869 Dihedral : 11.468 138.276 12968 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.25 % Favored : 90.73 % Rotamer: Outliers : 0.41 % Allowed : 1.28 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.11), residues: 4077 helix: -2.01 (0.08), residues: 2332 sheet: -2.84 (0.25), residues: 354 loop : -2.76 (0.14), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 596 TYR 0.068 0.003 TYR E 661 PHE 0.038 0.005 PHE B 709 TRP 0.043 0.005 TRP E 543 HIS 0.018 0.003 HIS F 747 Details of bonding type rmsd covalent geometry : bond 0.01152 (33285) covalent geometry : angle 1.24525 (44929) hydrogen bonds : bond 0.14366 ( 1838) hydrogen bonds : angle 7.62748 ( 5427) Misc. bond : bond 0.00849 ( 19) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1066 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7907 (mmp) cc_final: 0.7433 (mmp) REVERT: A 318 GLU cc_start: 0.8139 (mp0) cc_final: 0.7859 (mp0) REVERT: A 631 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7305 (ttm-80) REVERT: A 645 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7738 (ttm110) REVERT: A 661 TYR cc_start: 0.7165 (t80) cc_final: 0.6848 (t80) REVERT: A 673 VAL cc_start: 0.9093 (t) cc_final: 0.8855 (p) REVERT: A 749 PHE cc_start: 0.7611 (m-10) cc_final: 0.7014 (m-10) REVERT: A 776 GLN cc_start: 0.8851 (mt0) cc_final: 0.8472 (tp40) REVERT: B 163 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8238 (mtmt) REVERT: B 201 ASN cc_start: 0.6804 (m-40) cc_final: 0.6523 (m-40) REVERT: B 265 ASP cc_start: 0.8429 (m-30) cc_final: 0.7798 (m-30) REVERT: B 275 LEU cc_start: 0.9535 (tp) cc_final: 0.9288 (tt) REVERT: B 299 LEU cc_start: 0.9181 (mp) cc_final: 0.8936 (mt) REVERT: B 310 CYS cc_start: 0.7111 (t) cc_final: 0.6484 (t) REVERT: B 430 MET cc_start: 0.3692 (mmm) cc_final: 0.3020 (ttm) REVERT: B 587 SER cc_start: 0.9014 (t) cc_final: 0.8786 (p) REVERT: B 615 CYS cc_start: 0.8367 (m) cc_final: 0.8098 (t) REVERT: B 627 GLU cc_start: 0.7659 (mp0) cc_final: 0.7291 (tm-30) REVERT: B 629 MET cc_start: 0.8030 (ptm) cc_final: 0.7624 (ppp) REVERT: B 634 MET cc_start: 0.8309 (mmm) cc_final: 0.8033 (mmm) REVERT: B 719 ASN cc_start: 0.8199 (p0) cc_final: 0.7885 (m110) REVERT: B 758 ASP cc_start: 0.7426 (t0) cc_final: 0.6848 (m-30) REVERT: B 821 ILE cc_start: 0.8869 (mt) cc_final: 0.8526 (mm) REVERT: B 846 LEU cc_start: 0.9372 (mt) cc_final: 0.9103 (tt) REVERT: C 196 ARG cc_start: 0.8618 (mtp180) cc_final: 0.8017 (mtm-85) REVERT: C 246 VAL cc_start: 0.7622 (t) cc_final: 0.7282 (m) REVERT: C 257 GLU cc_start: 0.8554 (tt0) cc_final: 0.8092 (tm-30) REVERT: C 268 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8499 (tptt) REVERT: C 318 GLU cc_start: 0.8466 (mp0) cc_final: 0.7887 (mp0) REVERT: C 498 MET cc_start: 0.4996 (mmm) cc_final: 0.4714 (mmm) REVERT: C 602 LEU cc_start: 0.8887 (tp) cc_final: 0.8618 (tt) REVERT: C 615 CYS cc_start: 0.9154 (m) cc_final: 0.8361 (t) REVERT: C 638 MET cc_start: 0.8518 (mtm) cc_final: 0.8283 (mtm) REVERT: C 821 ILE cc_start: 0.8299 (mt) cc_final: 0.8098 (mm) REVERT: C 827 ASN cc_start: 0.9264 (m-40) cc_final: 0.8989 (m-40) REVERT: D 180 VAL cc_start: 0.8320 (t) cc_final: 0.8062 (p) REVERT: D 274 ILE cc_start: 0.8103 (mt) cc_final: 0.7782 (mm) REVERT: D 323 ILE cc_start: 0.8089 (mt) cc_final: 0.7882 (mm) REVERT: D 358 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7683 (pp20) REVERT: D 395 ASP cc_start: 0.8768 (t0) cc_final: 0.8269 (t0) REVERT: D 524 MET cc_start: 0.5121 (mmm) cc_final: 0.4588 (mmt) REVERT: D 630 VAL cc_start: 0.8618 (t) cc_final: 0.8312 (t) REVERT: D 691 LEU cc_start: 0.8101 (mt) cc_final: 0.7650 (mt) REVERT: D 760 VAL cc_start: 0.8492 (t) cc_final: 0.8000 (p) REVERT: D 774 ILE cc_start: 0.9058 (mt) cc_final: 0.8716 (tp) REVERT: D 792 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7616 (mp0) REVERT: D 834 LEU cc_start: 0.9041 (mt) cc_final: 0.8770 (mt) REVERT: E 319 TYR cc_start: 0.8508 (t80) cc_final: 0.8218 (t80) REVERT: E 335 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8246 (tptp) REVERT: E 370 ILE cc_start: 0.8177 (mt) cc_final: 0.7900 (mt) REVERT: E 540 LEU cc_start: 0.8636 (tp) cc_final: 0.8419 (tt) REVERT: E 562 MET cc_start: 0.8432 (tpt) cc_final: 0.8181 (tpt) REVERT: E 591 LEU cc_start: 0.8535 (mp) cc_final: 0.8313 (mp) REVERT: E 621 PHE cc_start: 0.8223 (t80) cc_final: 0.7818 (t80) REVERT: E 691 LEU cc_start: 0.8476 (mt) cc_final: 0.7967 (tp) REVERT: E 701 ASP cc_start: 0.8802 (p0) cc_final: 0.8283 (p0) REVERT: E 784 LYS cc_start: 0.9177 (tttt) cc_final: 0.8940 (tmmt) REVERT: E 817 LEU cc_start: 0.8826 (tp) cc_final: 0.8612 (tp) REVERT: F 242 MET cc_start: 0.6249 (mmp) cc_final: 0.5824 (tpp) REVERT: F 319 TYR cc_start: 0.7514 (t80) cc_final: 0.6816 (t80) REVERT: F 322 TYR cc_start: 0.7298 (m-10) cc_final: 0.6909 (m-10) REVERT: F 324 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6164 (pp20) REVERT: F 333 PHE cc_start: 0.7355 (m-80) cc_final: 0.7149 (m-10) REVERT: F 456 SER cc_start: 0.9119 (t) cc_final: 0.8764 (p) REVERT: F 457 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8389 (tm-30) REVERT: F 462 TRP cc_start: 0.7601 (t60) cc_final: 0.6524 (t60) REVERT: F 476 LYS cc_start: 0.7589 (ttmt) cc_final: 0.7156 (tptp) REVERT: F 603 PHE cc_start: 0.7742 (m-10) cc_final: 0.7180 (m-10) REVERT: F 613 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8063 (tt0) REVERT: F 614 LEU cc_start: 0.8421 (tp) cc_final: 0.8087 (mt) REVERT: F 797 ASP cc_start: 0.8109 (m-30) cc_final: 0.7901 (p0) REVERT: F 801 LYS cc_start: 0.9394 (mtpp) cc_final: 0.8953 (mttt) outliers start: 14 outliers final: 3 residues processed: 1079 average time/residue: 0.2344 time to fit residues: 388.2604 Evaluate side-chains 577 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 574 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 334 GLN A 362 HIS ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 334 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 HIS B 831 GLN B 858 HIS C 192 GLN C 454 GLN C 512 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN C 822 GLN C 849 ASN D 281 HIS D 512 GLN D 641 HIS D 747 HIS ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 823 GLN D 849 ASN E 221 GLN E 269 GLN E 297 ASN ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 GLN E 764 HIS E 794 HIS E 822 GLN ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS F 778 GLN F 849 ASN F 858 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.131164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.105091 restraints weight = 102436.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.106856 restraints weight = 69655.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.107274 restraints weight = 50482.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.107595 restraints weight = 45662.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107754 restraints weight = 41419.685| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33304 Z= 0.200 Angle : 0.784 23.294 44929 Z= 0.396 Chirality : 0.045 0.253 5088 Planarity : 0.006 0.081 5869 Dihedral : 9.898 125.511 4748 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.12), residues: 4077 helix: -0.55 (0.10), residues: 2349 sheet: -2.75 (0.25), residues: 345 loop : -2.20 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 414 TYR 0.023 0.002 TYR C 653 PHE 0.018 0.002 PHE F 603 TRP 0.024 0.003 TRP C 543 HIS 0.007 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00421 (33285) covalent geometry : angle 0.78399 (44929) hydrogen bonds : bond 0.05111 ( 1838) hydrogen bonds : angle 5.88809 ( 5427) Misc. bond : bond 0.00798 ( 19) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 733 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7818 (mmp) cc_final: 0.7522 (mmp) REVERT: A 320 ARG cc_start: 0.8076 (ptp-170) cc_final: 0.7764 (ttm110) REVERT: A 346 THR cc_start: 0.9279 (m) cc_final: 0.8993 (p) REVERT: A 561 ARG cc_start: 0.8491 (ptt180) cc_final: 0.8025 (mmt180) REVERT: A 631 ARG cc_start: 0.7757 (ttt180) cc_final: 0.7119 (ttm-80) REVERT: A 673 VAL cc_start: 0.8720 (t) cc_final: 0.8248 (p) REVERT: A 776 GLN cc_start: 0.8784 (mt0) cc_final: 0.8557 (tp40) REVERT: B 201 ASN cc_start: 0.7237 (m-40) cc_final: 0.6935 (m-40) REVERT: B 318 GLU cc_start: 0.6342 (mp0) cc_final: 0.6053 (mp0) REVERT: B 320 ARG cc_start: 0.7946 (ttp-110) cc_final: 0.7707 (ttm170) REVERT: B 361 HIS cc_start: 0.7236 (m-70) cc_final: 0.7005 (m-70) REVERT: B 430 MET cc_start: 0.3448 (mmm) cc_final: 0.1932 (tmm) REVERT: B 531 VAL cc_start: 0.7783 (t) cc_final: 0.7533 (t) REVERT: B 615 CYS cc_start: 0.7898 (m) cc_final: 0.7640 (t) REVERT: B 782 LEU cc_start: 0.9401 (tp) cc_final: 0.9123 (tt) REVERT: B 846 LEU cc_start: 0.9247 (mt) cc_final: 0.9019 (tt) REVERT: C 232 LEU cc_start: 0.8975 (mt) cc_final: 0.8728 (mt) REVERT: C 257 GLU cc_start: 0.8221 (tt0) cc_final: 0.7780 (tm-30) REVERT: C 260 LYS cc_start: 0.8480 (tttt) cc_final: 0.8091 (mmtt) REVERT: C 498 MET cc_start: 0.5163 (mmm) cc_final: 0.4613 (mmm) REVERT: C 644 SER cc_start: 0.8590 (m) cc_final: 0.8094 (t) REVERT: C 827 ASN cc_start: 0.8966 (m-40) cc_final: 0.8571 (m-40) REVERT: D 358 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7639 (mm-30) REVERT: D 524 MET cc_start: 0.5159 (mmm) cc_final: 0.4469 (mmt) REVERT: D 691 LEU cc_start: 0.7784 (mt) cc_final: 0.6307 (mt) REVERT: D 774 ILE cc_start: 0.8964 (mt) cc_final: 0.8533 (tp) REVERT: E 540 LEU cc_start: 0.8299 (tp) cc_final: 0.8094 (tt) REVERT: E 562 MET cc_start: 0.8541 (tpt) cc_final: 0.8285 (tpp) REVERT: E 621 PHE cc_start: 0.8238 (t80) cc_final: 0.7659 (t80) REVERT: E 701 ASP cc_start: 0.8399 (p0) cc_final: 0.7809 (t70) REVERT: F 381 ILE cc_start: 0.7841 (mp) cc_final: 0.7574 (mp) REVERT: F 462 TRP cc_start: 0.7860 (t60) cc_final: 0.6449 (t60) REVERT: F 512 GLN cc_start: 0.7262 (tm-30) cc_final: 0.6384 (pt0) REVERT: F 564 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8042 (tp-100) REVERT: F 614 LEU cc_start: 0.8354 (tp) cc_final: 0.7847 (mt) REVERT: F 777 ILE cc_start: 0.8468 (mt) cc_final: 0.8042 (mt) REVERT: F 801 LYS cc_start: 0.9426 (mtpp) cc_final: 0.9054 (mtpt) outliers start: 4 outliers final: 1 residues processed: 736 average time/residue: 0.2249 time to fit residues: 262.3541 Evaluate side-chains 475 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 474 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 284 optimal weight: 30.0000 chunk 225 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 334 GLN A 512 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 HIS A 806 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 ASN B 770 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 361 HIS C 378 HIS C 512 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 512 GLN ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 823 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 858 HIS ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 567 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.129279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103621 restraints weight = 105873.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105113 restraints weight = 74358.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107223 restraints weight = 51105.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.106815 restraints weight = 41831.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106584 restraints weight = 37077.749| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 33304 Z= 0.195 Angle : 0.741 24.371 44929 Z= 0.373 Chirality : 0.045 0.236 5088 Planarity : 0.006 0.064 5869 Dihedral : 9.458 127.036 4748 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 4077 helix: 0.02 (0.10), residues: 2387 sheet: -2.64 (0.25), residues: 353 loop : -2.02 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 497 TYR 0.018 0.001 TYR E 671 PHE 0.024 0.002 PHE F 709 TRP 0.013 0.002 TRP D 462 HIS 0.015 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00422 (33285) covalent geometry : angle 0.74124 (44929) hydrogen bonds : bond 0.04680 ( 1838) hydrogen bonds : angle 5.51282 ( 5427) Misc. bond : bond 0.00492 ( 19) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 639 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4239 (tpp) cc_final: 0.3490 (mmm) REVERT: A 318 GLU cc_start: 0.7634 (mp0) cc_final: 0.7231 (mp0) REVERT: A 320 ARG cc_start: 0.8313 (ptp-170) cc_final: 0.8031 (ttm110) REVERT: A 498 MET cc_start: 0.0585 (mmm) cc_final: 0.0273 (mtt) REVERT: A 525 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.6873 (tpt170) REVERT: A 561 ARG cc_start: 0.8519 (ptt180) cc_final: 0.8048 (mmt180) REVERT: A 588 ARG cc_start: 0.7512 (mmt90) cc_final: 0.7108 (tmt170) REVERT: A 631 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7183 (ttm-80) REVERT: A 673 VAL cc_start: 0.8839 (t) cc_final: 0.8126 (p) REVERT: A 776 GLN cc_start: 0.8857 (mt0) cc_final: 0.8560 (tp40) REVERT: B 300 LYS cc_start: 0.8766 (tttt) cc_final: 0.8480 (ttpp) REVERT: B 332 ARG cc_start: 0.8420 (mmt-90) cc_final: 0.7183 (mmt-90) REVERT: B 361 HIS cc_start: 0.7584 (m-70) cc_final: 0.7136 (m-70) REVERT: B 403 MET cc_start: 0.7487 (tpp) cc_final: 0.6705 (tpp) REVERT: B 430 MET cc_start: 0.3306 (mmm) cc_final: 0.1932 (tmm) REVERT: B 615 CYS cc_start: 0.7950 (m) cc_final: 0.7656 (t) REVERT: B 622 MET cc_start: 0.7429 (tpp) cc_final: 0.7223 (tpp) REVERT: B 782 LEU cc_start: 0.9526 (tp) cc_final: 0.9265 (tp) REVERT: B 791 TYR cc_start: 0.6281 (m-80) cc_final: 0.5987 (m-80) REVERT: B 846 LEU cc_start: 0.9390 (mt) cc_final: 0.9091 (tt) REVERT: C 177 LEU cc_start: 0.8411 (tp) cc_final: 0.8173 (tp) REVERT: C 232 LEU cc_start: 0.9159 (mt) cc_final: 0.8856 (mt) REVERT: C 257 GLU cc_start: 0.8393 (tt0) cc_final: 0.7885 (tm-30) REVERT: C 260 LYS cc_start: 0.8443 (tttt) cc_final: 0.8121 (mmtt) REVERT: C 280 LEU cc_start: 0.8806 (tp) cc_final: 0.8546 (tp) REVERT: C 283 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7761 (mtm) REVERT: C 396 GLU cc_start: 0.8147 (tp30) cc_final: 0.7927 (tp30) REVERT: C 498 MET cc_start: 0.5088 (mmm) cc_final: 0.4614 (mmm) REVERT: C 524 MET cc_start: 0.1502 (ttt) cc_final: 0.0950 (ttp) REVERT: C 615 CYS cc_start: 0.8795 (m) cc_final: 0.8296 (t) REVERT: C 827 ASN cc_start: 0.9133 (m-40) cc_final: 0.8755 (m-40) REVERT: D 293 MET cc_start: 0.7238 (ttm) cc_final: 0.6954 (ttm) REVERT: D 358 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7723 (mm-30) REVERT: D 524 MET cc_start: 0.5205 (mmm) cc_final: 0.4462 (mmt) REVERT: D 677 ASP cc_start: 0.6587 (t0) cc_final: 0.6353 (t0) REVERT: D 723 ASP cc_start: 0.7604 (p0) cc_final: 0.7397 (p0) REVERT: D 725 ILE cc_start: 0.9097 (mt) cc_final: 0.8809 (mt) REVERT: D 774 ILE cc_start: 0.9157 (mt) cc_final: 0.8778 (tp) REVERT: E 283 MET cc_start: 0.8440 (tmm) cc_final: 0.8089 (tmm) REVERT: E 311 VAL cc_start: 0.9200 (t) cc_final: 0.8990 (m) REVERT: E 517 THR cc_start: 0.7557 (m) cc_final: 0.7195 (p) REVERT: E 552 MET cc_start: 0.7496 (pmm) cc_final: 0.7147 (pmm) REVERT: E 638 MET cc_start: 0.8126 (pmm) cc_final: 0.7191 (ptm) REVERT: E 780 LYS cc_start: 0.8714 (mptt) cc_final: 0.8509 (mmtm) REVERT: E 817 LEU cc_start: 0.9114 (tp) cc_final: 0.8607 (tp) REVERT: E 821 ILE cc_start: 0.8634 (mm) cc_final: 0.8367 (pt) REVERT: F 456 SER cc_start: 0.8899 (p) cc_final: 0.8699 (p) REVERT: F 512 GLN cc_start: 0.7432 (tm-30) cc_final: 0.6594 (pt0) REVERT: F 564 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8017 (tp-100) REVERT: F 716 MET cc_start: 0.9169 (mpp) cc_final: 0.8715 (mpp) REVERT: F 801 LYS cc_start: 0.9421 (mtpp) cc_final: 0.8991 (mtpt) outliers start: 3 outliers final: 0 residues processed: 641 average time/residue: 0.2026 time to fit residues: 212.5475 Evaluate side-chains 437 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 chunk 308 optimal weight: 0.4980 chunk 113 optimal weight: 0.1980 chunk 297 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 334 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN B 770 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN C 858 HIS D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.129239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.102111 restraints weight = 105798.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.103774 restraints weight = 69430.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104925 restraints weight = 52482.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105657 restraints weight = 43549.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.105921 restraints weight = 39017.537| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33304 Z= 0.187 Angle : 0.730 22.401 44929 Z= 0.367 Chirality : 0.044 0.224 5088 Planarity : 0.005 0.059 5869 Dihedral : 9.276 127.437 4748 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 4077 helix: 0.26 (0.10), residues: 2398 sheet: -2.45 (0.24), residues: 385 loop : -1.96 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 379 TYR 0.018 0.002 TYR A 357 PHE 0.027 0.002 PHE E 621 TRP 0.011 0.002 TRP B 462 HIS 0.005 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00408 (33285) covalent geometry : angle 0.73044 (44929) hydrogen bonds : bond 0.04518 ( 1838) hydrogen bonds : angle 5.39553 ( 5427) Misc. bond : bond 0.00565 ( 19) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4674 (tpp) cc_final: 0.4031 (mmt) REVERT: A 311 VAL cc_start: 0.8238 (t) cc_final: 0.8004 (t) REVERT: A 508 GLU cc_start: 0.2993 (pt0) cc_final: 0.2767 (mt-10) REVERT: A 525 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.6994 (tpt170) REVERT: A 561 ARG cc_start: 0.8404 (ptt180) cc_final: 0.8045 (mmt180) REVERT: A 588 ARG cc_start: 0.7350 (mmt90) cc_final: 0.7128 (tmt170) REVERT: A 629 MET cc_start: 0.7171 (ppp) cc_final: 0.6965 (ppp) REVERT: A 631 ARG cc_start: 0.7644 (ttt180) cc_final: 0.7153 (ttm-80) REVERT: A 673 VAL cc_start: 0.8807 (t) cc_final: 0.8107 (p) REVERT: A 776 GLN cc_start: 0.8881 (mt0) cc_final: 0.8547 (tp40) REVERT: B 332 ARG cc_start: 0.8492 (mmt-90) cc_final: 0.7279 (mmt-90) REVERT: B 361 HIS cc_start: 0.7725 (m-70) cc_final: 0.7261 (m-70) REVERT: B 403 MET cc_start: 0.7498 (tpp) cc_final: 0.7004 (tpp) REVERT: B 430 MET cc_start: 0.3202 (mmm) cc_final: 0.1927 (tmm) REVERT: B 782 LEU cc_start: 0.9295 (tp) cc_final: 0.9031 (tp) REVERT: B 846 LEU cc_start: 0.9283 (mt) cc_final: 0.8987 (tt) REVERT: C 196 ARG cc_start: 0.8019 (mtp-110) cc_final: 0.7685 (mtm-85) REVERT: C 257 GLU cc_start: 0.8393 (tt0) cc_final: 0.7795 (tm-30) REVERT: C 283 MET cc_start: 0.7903 (mpp) cc_final: 0.7431 (mtm) REVERT: C 318 GLU cc_start: 0.7665 (mp0) cc_final: 0.7066 (mm-30) REVERT: C 498 MET cc_start: 0.5113 (mmm) cc_final: 0.4638 (mmm) REVERT: C 524 MET cc_start: 0.1675 (ttt) cc_final: 0.0822 (ttp) REVERT: C 615 CYS cc_start: 0.8669 (m) cc_final: 0.8237 (t) REVERT: C 827 ASN cc_start: 0.9030 (m-40) cc_final: 0.8634 (m-40) REVERT: D 204 LEU cc_start: 0.8697 (mm) cc_final: 0.8485 (mm) REVERT: D 317 ASP cc_start: 0.7595 (p0) cc_final: 0.7358 (p0) REVERT: D 524 MET cc_start: 0.5292 (mmm) cc_final: 0.4464 (mmt) REVERT: D 677 ASP cc_start: 0.6540 (t0) cc_final: 0.6257 (t0) REVERT: D 691 LEU cc_start: 0.7846 (mt) cc_final: 0.7486 (mt) REVERT: D 723 ASP cc_start: 0.7615 (p0) cc_final: 0.7320 (p0) REVERT: E 517 THR cc_start: 0.7609 (m) cc_final: 0.7298 (p) REVERT: E 552 MET cc_start: 0.7424 (pmm) cc_final: 0.6787 (pmm) REVERT: E 562 MET cc_start: 0.8817 (tpp) cc_final: 0.8440 (tpt) REVERT: E 621 PHE cc_start: 0.8273 (t80) cc_final: 0.8046 (t80) REVERT: E 638 MET cc_start: 0.7930 (pmm) cc_final: 0.7239 (ptm) REVERT: E 817 LEU cc_start: 0.9172 (tp) cc_final: 0.8914 (tp) REVERT: F 456 SER cc_start: 0.8896 (p) cc_final: 0.8665 (p) REVERT: F 716 MET cc_start: 0.9118 (mpp) cc_final: 0.8647 (mpp) REVERT: F 801 LYS cc_start: 0.9329 (mtpp) cc_final: 0.8926 (mtpt) outliers start: 1 outliers final: 0 residues processed: 591 average time/residue: 0.2010 time to fit residues: 196.3430 Evaluate side-chains 403 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 6 optimal weight: 5.9990 chunk 405 optimal weight: 0.3980 chunk 406 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 350 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 256 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN B 770 HIS B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN C 832 GLN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS E 824 GLN F 378 HIS F 454 GLN F 806 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.129513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.103715 restraints weight = 107908.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.105721 restraints weight = 73144.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.105841 restraints weight = 49715.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.106207 restraints weight = 49358.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.106317 restraints weight = 44020.997| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 33304 Z= 0.154 Angle : 0.691 21.325 44929 Z= 0.346 Chirality : 0.044 0.184 5088 Planarity : 0.005 0.059 5869 Dihedral : 9.038 123.383 4748 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4077 helix: 0.56 (0.10), residues: 2379 sheet: -2.18 (0.25), residues: 375 loop : -1.78 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 789 TYR 0.016 0.001 TYR F 319 PHE 0.022 0.002 PHE D 623 TRP 0.011 0.002 TRP B 462 HIS 0.010 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00331 (33285) covalent geometry : angle 0.69110 (44929) hydrogen bonds : bond 0.04181 ( 1838) hydrogen bonds : angle 5.18439 ( 5427) Misc. bond : bond 0.00494 ( 19) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 574 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4565 (tpp) cc_final: 0.3876 (mmt) REVERT: A 525 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7026 (tpt170) REVERT: A 561 ARG cc_start: 0.8622 (ptt180) cc_final: 0.8096 (mmt180) REVERT: A 588 ARG cc_start: 0.7503 (mmt90) cc_final: 0.7265 (tmt170) REVERT: A 631 ARG cc_start: 0.7717 (ttt180) cc_final: 0.7228 (ttm-80) REVERT: A 776 GLN cc_start: 0.8868 (mt0) cc_final: 0.8512 (tp40) REVERT: B 186 GLU cc_start: 0.8513 (mp0) cc_final: 0.7912 (mp0) REVERT: B 361 HIS cc_start: 0.7794 (m-70) cc_final: 0.7362 (m-70) REVERT: B 402 ARG cc_start: 0.7130 (ttp-170) cc_final: 0.6817 (ttp-170) REVERT: B 403 MET cc_start: 0.7469 (tpp) cc_final: 0.6722 (tpp) REVERT: B 430 MET cc_start: 0.2966 (mmm) cc_final: 0.1827 (tmm) REVERT: B 629 MET cc_start: 0.8469 (ppp) cc_final: 0.8237 (ppp) REVERT: B 782 LEU cc_start: 0.9335 (tp) cc_final: 0.9067 (tp) REVERT: B 846 LEU cc_start: 0.9393 (mt) cc_final: 0.9067 (tt) REVERT: C 196 ARG cc_start: 0.8040 (mtp-110) cc_final: 0.7785 (mtm-85) REVERT: C 257 GLU cc_start: 0.8413 (tt0) cc_final: 0.7919 (tm-30) REVERT: C 498 MET cc_start: 0.5208 (mmm) cc_final: 0.4691 (mmm) REVERT: C 524 MET cc_start: 0.1493 (ttt) cc_final: 0.0899 (ttp) REVERT: C 615 CYS cc_start: 0.8696 (m) cc_final: 0.8185 (t) REVERT: C 716 MET cc_start: 0.6930 (mtp) cc_final: 0.6721 (ttm) REVERT: C 827 ASN cc_start: 0.9136 (m-40) cc_final: 0.8694 (m-40) REVERT: D 524 MET cc_start: 0.5325 (mmm) cc_final: 0.4545 (mmt) REVERT: D 677 ASP cc_start: 0.6659 (t0) cc_final: 0.6451 (t0) REVERT: D 691 LEU cc_start: 0.7884 (mt) cc_final: 0.7550 (mt) REVERT: D 723 ASP cc_start: 0.7794 (p0) cc_final: 0.7505 (p0) REVERT: D 834 LEU cc_start: 0.8829 (mm) cc_final: 0.8563 (mm) REVERT: E 195 GLN cc_start: 0.7971 (pt0) cc_final: 0.7117 (mm-40) REVERT: E 317 ASP cc_start: 0.8111 (p0) cc_final: 0.7497 (p0) REVERT: E 517 THR cc_start: 0.7538 (m) cc_final: 0.7275 (p) REVERT: E 546 ILE cc_start: 0.8693 (mm) cc_final: 0.8467 (mm) REVERT: E 562 MET cc_start: 0.8535 (tpp) cc_final: 0.8189 (tpp) REVERT: E 621 PHE cc_start: 0.8314 (t80) cc_final: 0.7995 (t80) REVERT: E 638 MET cc_start: 0.8193 (pmm) cc_final: 0.7657 (ptm) REVERT: E 687 PHE cc_start: 0.8134 (m-10) cc_final: 0.7736 (m-80) REVERT: E 817 LEU cc_start: 0.9227 (tp) cc_final: 0.8981 (tp) REVERT: F 330 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6270 (tp30) outliers start: 3 outliers final: 0 residues processed: 576 average time/residue: 0.1955 time to fit residues: 186.3491 Evaluate side-chains 410 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 153 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 400 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 770 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 HIS ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 174 GLN D 201 ASN D 281 HIS D 488 GLN ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.123041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095308 restraints weight = 114885.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.097560 restraints weight = 70014.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.099105 restraints weight = 49688.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.100089 restraints weight = 39531.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.100597 restraints weight = 34174.049| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33304 Z= 0.175 Angle : 0.705 20.946 44929 Z= 0.352 Chirality : 0.044 0.212 5088 Planarity : 0.005 0.059 5869 Dihedral : 8.961 119.430 4748 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4077 helix: 0.62 (0.10), residues: 2409 sheet: -2.06 (0.25), residues: 385 loop : -1.66 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 491 TYR 0.024 0.001 TYR F 656 PHE 0.023 0.002 PHE F 621 TRP 0.010 0.002 TRP E 462 HIS 0.014 0.001 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00384 (33285) covalent geometry : angle 0.70504 (44929) hydrogen bonds : bond 0.04192 ( 1838) hydrogen bonds : angle 5.13988 ( 5427) Misc. bond : bond 0.00505 ( 19) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.6567 (tt0) cc_final: 0.6267 (mp0) REVERT: A 277 ILE cc_start: 0.8597 (mt) cc_final: 0.8322 (mm) REVERT: A 293 MET cc_start: 0.4455 (tpp) cc_final: 0.3895 (mmt) REVERT: A 525 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.7133 (tpt170) REVERT: A 561 ARG cc_start: 0.8343 (ptt180) cc_final: 0.8024 (mmt180) REVERT: A 624 ASP cc_start: 0.7247 (m-30) cc_final: 0.6858 (p0) REVERT: A 631 ARG cc_start: 0.7957 (ttt180) cc_final: 0.7341 (ttm-80) REVERT: A 776 GLN cc_start: 0.8817 (mt0) cc_final: 0.8560 (tp40) REVERT: B 361 HIS cc_start: 0.7895 (m-70) cc_final: 0.7416 (m-70) REVERT: B 402 ARG cc_start: 0.7120 (ttp-170) cc_final: 0.6822 (ttp-170) REVERT: B 403 MET cc_start: 0.7645 (tpp) cc_final: 0.7163 (tpp) REVERT: B 430 MET cc_start: 0.2813 (mmm) cc_final: 0.1704 (tmm) REVERT: B 629 MET cc_start: 0.8539 (ppp) cc_final: 0.8243 (ppp) REVERT: B 737 MET cc_start: 0.7176 (mmm) cc_final: 0.6942 (mmm) REVERT: B 782 LEU cc_start: 0.9256 (tp) cc_final: 0.8972 (tp) REVERT: B 846 LEU cc_start: 0.9500 (mt) cc_final: 0.9105 (tt) REVERT: C 196 ARG cc_start: 0.8128 (mtp-110) cc_final: 0.7812 (mtm-85) REVERT: C 257 GLU cc_start: 0.8397 (tt0) cc_final: 0.7911 (tm-30) REVERT: C 396 GLU cc_start: 0.8099 (tp30) cc_final: 0.7836 (tp30) REVERT: C 498 MET cc_start: 0.5267 (mmm) cc_final: 0.4762 (mmm) REVERT: C 524 MET cc_start: 0.1576 (ttt) cc_final: 0.1055 (ttp) REVERT: C 615 CYS cc_start: 0.8825 (m) cc_final: 0.8322 (t) REVERT: C 827 ASN cc_start: 0.9185 (m-40) cc_final: 0.8730 (m-40) REVERT: D 204 LEU cc_start: 0.8944 (mm) cc_final: 0.8722 (mm) REVERT: D 317 ASP cc_start: 0.8186 (p0) cc_final: 0.7956 (p0) REVERT: D 524 MET cc_start: 0.5487 (mmm) cc_final: 0.4322 (mmt) REVERT: D 675 LEU cc_start: 0.8618 (tt) cc_final: 0.8209 (tp) REVERT: E 195 GLN cc_start: 0.8141 (pt0) cc_final: 0.7166 (mm-40) REVERT: E 315 THR cc_start: 0.9173 (p) cc_final: 0.8901 (t) REVERT: E 350 LEU cc_start: 0.9129 (mm) cc_final: 0.8673 (tp) REVERT: E 517 THR cc_start: 0.7534 (m) cc_final: 0.7273 (p) REVERT: E 562 MET cc_start: 0.8083 (tpp) cc_final: 0.7565 (tpt) REVERT: E 638 MET cc_start: 0.8298 (pmm) cc_final: 0.7536 (ptm) REVERT: E 687 PHE cc_start: 0.8341 (m-10) cc_final: 0.7859 (m-80) REVERT: E 817 LEU cc_start: 0.9246 (tp) cc_final: 0.8991 (tp) REVERT: F 240 LEU cc_start: 0.7069 (tp) cc_final: 0.6671 (tt) REVERT: F 298 MET cc_start: 0.6002 (mmm) cc_final: 0.5506 (mmt) REVERT: F 330 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6200 (tp30) REVERT: F 498 MET cc_start: 0.6356 (tpp) cc_final: 0.5846 (tpp) REVERT: F 629 MET cc_start: 0.8433 (ppp) cc_final: 0.7969 (ppp) REVERT: F 662 LEU cc_start: 0.7467 (tp) cc_final: 0.7249 (tt) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.2009 time to fit residues: 185.6601 Evaluate side-chains 395 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 374 optimal weight: 30.0000 chunk 386 optimal weight: 0.0870 chunk 93 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 366 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 770 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 174 GLN D 201 ASN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 HIS ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.128319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101276 restraints weight = 107183.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103089 restraints weight = 69193.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.104398 restraints weight = 51414.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104895 restraints weight = 42201.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.105340 restraints weight = 38103.607| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33304 Z= 0.201 Angle : 0.740 20.443 44929 Z= 0.370 Chirality : 0.045 0.185 5088 Planarity : 0.005 0.101 5869 Dihedral : 9.058 119.207 4748 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.03 % Allowed : 1.66 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4077 helix: 0.65 (0.10), residues: 2401 sheet: -2.00 (0.25), residues: 389 loop : -1.68 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 491 TYR 0.019 0.002 TYR F 656 PHE 0.026 0.002 PHE D 621 TRP 0.011 0.002 TRP E 462 HIS 0.016 0.001 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00440 (33285) covalent geometry : angle 0.74006 (44929) hydrogen bonds : bond 0.04306 ( 1838) hydrogen bonds : angle 5.16982 ( 5427) Misc. bond : bond 0.00576 ( 19) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 533 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4727 (tpp) cc_final: 0.4288 (mmt) REVERT: A 318 GLU cc_start: 0.7688 (mp0) cc_final: 0.7364 (mp0) REVERT: A 405 ILE cc_start: 0.7782 (pt) cc_final: 0.7551 (tp) REVERT: A 525 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7206 (tpt170) REVERT: A 561 ARG cc_start: 0.8545 (ptt180) cc_final: 0.8087 (mmt180) REVERT: A 624 ASP cc_start: 0.7315 (m-30) cc_final: 0.6924 (p0) REVERT: A 631 ARG cc_start: 0.7904 (ttt180) cc_final: 0.7394 (ttm-80) REVERT: A 776 GLN cc_start: 0.8914 (mt0) cc_final: 0.8642 (tp40) REVERT: B 361 HIS cc_start: 0.7969 (m-70) cc_final: 0.7576 (m-70) REVERT: B 402 ARG cc_start: 0.7085 (ttp-170) cc_final: 0.6830 (ttp-170) REVERT: B 403 MET cc_start: 0.7608 (tpp) cc_final: 0.7279 (tpp) REVERT: B 430 MET cc_start: 0.2569 (mmm) cc_final: 0.1870 (ttm) REVERT: B 629 MET cc_start: 0.8608 (ppp) cc_final: 0.8308 (ppp) REVERT: B 782 LEU cc_start: 0.9194 (tp) cc_final: 0.8931 (tp) REVERT: B 846 LEU cc_start: 0.9310 (mt) cc_final: 0.8992 (tp) REVERT: C 180 VAL cc_start: 0.8730 (t) cc_final: 0.8525 (p) REVERT: C 196 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7919 (mtm-85) REVERT: C 257 GLU cc_start: 0.8505 (tt0) cc_final: 0.7968 (tm-30) REVERT: C 498 MET cc_start: 0.5171 (mmm) cc_final: 0.4915 (tpp) REVERT: C 615 CYS cc_start: 0.8852 (m) cc_final: 0.8388 (t) REVERT: C 716 MET cc_start: 0.7185 (mtp) cc_final: 0.6881 (ttm) REVERT: C 827 ASN cc_start: 0.9178 (m-40) cc_final: 0.8690 (m-40) REVERT: D 524 MET cc_start: 0.5388 (mmm) cc_final: 0.4448 (mmt) REVERT: D 691 LEU cc_start: 0.8065 (mm) cc_final: 0.7800 (mm) REVERT: D 723 ASP cc_start: 0.8025 (p0) cc_final: 0.7748 (p0) REVERT: E 195 GLN cc_start: 0.8090 (pt0) cc_final: 0.7170 (mm-40) REVERT: E 326 ASP cc_start: 0.8168 (t70) cc_final: 0.7872 (m-30) REVERT: E 475 ILE cc_start: 0.8302 (pt) cc_final: 0.8010 (pt) REVERT: E 517 THR cc_start: 0.7550 (m) cc_final: 0.7288 (p) REVERT: E 552 MET cc_start: 0.6955 (pmm) cc_final: 0.6455 (pmm) REVERT: E 562 MET cc_start: 0.7952 (tpp) cc_final: 0.7406 (tpp) REVERT: E 621 PHE cc_start: 0.8497 (t80) cc_final: 0.8030 (t80) REVERT: E 638 MET cc_start: 0.8314 (pmm) cc_final: 0.7358 (ptt) REVERT: E 687 PHE cc_start: 0.8345 (m-10) cc_final: 0.7889 (m-80) REVERT: E 708 ASP cc_start: 0.7107 (t0) cc_final: 0.6835 (p0) REVERT: E 817 LEU cc_start: 0.9319 (tp) cc_final: 0.9117 (tp) REVERT: F 240 LEU cc_start: 0.7023 (tp) cc_final: 0.6588 (tt) REVERT: F 330 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6443 (tp30) outliers start: 1 outliers final: 0 residues processed: 534 average time/residue: 0.1933 time to fit residues: 173.4861 Evaluate side-chains 380 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 154 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 244 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 355 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 175 optimal weight: 0.0020 chunk 115 optimal weight: 0.9980 overall best weight: 1.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 770 HIS B 849 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.131468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.106468 restraints weight = 111894.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.107747 restraints weight = 74351.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.108315 restraints weight = 57229.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109180 restraints weight = 46667.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109137 restraints weight = 40845.636| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33304 Z= 0.137 Angle : 0.698 18.909 44929 Z= 0.345 Chirality : 0.043 0.220 5088 Planarity : 0.005 0.059 5869 Dihedral : 8.827 117.114 4748 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 4077 helix: 0.93 (0.11), residues: 2387 sheet: -1.87 (0.25), residues: 396 loop : -1.62 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 756 TYR 0.018 0.001 TYR F 656 PHE 0.027 0.002 PHE D 621 TRP 0.011 0.001 TRP B 462 HIS 0.009 0.001 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00293 (33285) covalent geometry : angle 0.69756 (44929) hydrogen bonds : bond 0.04004 ( 1838) hydrogen bonds : angle 4.96119 ( 5427) Misc. bond : bond 0.00483 ( 19) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4670 (tpp) cc_final: 0.4114 (mmt) REVERT: A 525 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.7185 (tpt170) REVERT: A 561 ARG cc_start: 0.8315 (ptt180) cc_final: 0.8024 (mmt180) REVERT: A 631 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7379 (ttm-80) REVERT: A 776 GLN cc_start: 0.8741 (mt0) cc_final: 0.8519 (tp40) REVERT: B 361 HIS cc_start: 0.7882 (m-70) cc_final: 0.7413 (m-70) REVERT: B 402 ARG cc_start: 0.6863 (ttp-170) cc_final: 0.6631 (ttp-170) REVERT: B 403 MET cc_start: 0.7461 (tpp) cc_final: 0.6751 (tpp) REVERT: B 430 MET cc_start: 0.2561 (mmm) cc_final: 0.1878 (ttm) REVERT: B 629 MET cc_start: 0.8523 (ppp) cc_final: 0.8232 (ppp) REVERT: B 637 PHE cc_start: 0.8574 (m-10) cc_final: 0.8344 (m-10) REVERT: B 846 LEU cc_start: 0.9449 (mt) cc_final: 0.9055 (tt) REVERT: C 196 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7505 (mtm-85) REVERT: C 257 GLU cc_start: 0.8342 (tt0) cc_final: 0.7768 (tm-30) REVERT: C 498 MET cc_start: 0.5295 (mmm) cc_final: 0.5079 (tpp) REVERT: C 595 ASN cc_start: 0.5824 (p0) cc_final: 0.5464 (p0) REVERT: C 615 CYS cc_start: 0.8705 (m) cc_final: 0.8227 (t) REVERT: C 827 ASN cc_start: 0.8982 (m-40) cc_final: 0.8501 (m-40) REVERT: D 524 MET cc_start: 0.5294 (mmm) cc_final: 0.4192 (mmt) REVERT: D 675 LEU cc_start: 0.8595 (tt) cc_final: 0.8330 (tp) REVERT: E 443 MET cc_start: 0.6075 (tmm) cc_final: 0.3739 (mtt) REVERT: E 475 ILE cc_start: 0.8177 (pt) cc_final: 0.7848 (pt) REVERT: E 517 THR cc_start: 0.7393 (m) cc_final: 0.7148 (p) REVERT: E 552 MET cc_start: 0.7383 (pmm) cc_final: 0.6852 (pmm) REVERT: E 562 MET cc_start: 0.7646 (tpp) cc_final: 0.7049 (tpp) REVERT: E 621 PHE cc_start: 0.8428 (t80) cc_final: 0.8014 (t80) REVERT: E 638 MET cc_start: 0.8219 (pmm) cc_final: 0.7427 (ptt) REVERT: E 642 SER cc_start: 0.8747 (m) cc_final: 0.8472 (m) REVERT: E 679 VAL cc_start: 0.9088 (p) cc_final: 0.8880 (p) REVERT: E 687 PHE cc_start: 0.8117 (m-10) cc_final: 0.7661 (m-80) REVERT: E 817 LEU cc_start: 0.9164 (tp) cc_final: 0.8963 (tp) REVERT: F 167 ASP cc_start: 0.7389 (t0) cc_final: 0.6734 (t70) REVERT: F 240 LEU cc_start: 0.7129 (tp) cc_final: 0.6685 (tt) REVERT: F 330 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6376 (tp30) REVERT: F 401 ILE cc_start: 0.8478 (mm) cc_final: 0.8091 (mm) REVERT: F 629 MET cc_start: 0.8344 (ppp) cc_final: 0.7886 (ppp) REVERT: F 684 PRO cc_start: 0.6416 (Cg_exo) cc_final: 0.6195 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.1991 time to fit residues: 183.7805 Evaluate side-chains 387 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 246 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 320 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 370 optimal weight: 8.9990 chunk 202 optimal weight: 0.0570 chunk 15 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 321 optimal weight: 4.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN B 567 HIS B 770 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 HIS ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.121772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.098466 restraints weight = 111764.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.099521 restraints weight = 76160.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.100303 restraints weight = 52586.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.100347 restraints weight = 45262.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.100586 restraints weight = 43835.249| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33304 Z= 0.177 Angle : 0.736 19.323 44929 Z= 0.364 Chirality : 0.045 0.233 5088 Planarity : 0.005 0.058 5869 Dihedral : 8.893 116.603 4748 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 4077 helix: 0.82 (0.11), residues: 2411 sheet: -1.88 (0.25), residues: 390 loop : -1.60 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 497 TYR 0.018 0.002 TYR D 656 PHE 0.025 0.002 PHE E 637 TRP 0.009 0.001 TRP E 462 HIS 0.009 0.001 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00390 (33285) covalent geometry : angle 0.73559 (44929) hydrogen bonds : bond 0.04173 ( 1838) hydrogen bonds : angle 5.05995 ( 5427) Misc. bond : bond 0.00494 ( 19) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4350 (tpp) cc_final: 0.3966 (mmt) REVERT: A 315 THR cc_start: 0.8639 (p) cc_final: 0.7275 (p) REVERT: A 318 GLU cc_start: 0.7762 (mp0) cc_final: 0.7038 (mp0) REVERT: A 358 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6794 (mt-10) REVERT: A 525 ARG cc_start: 0.7689 (mmm-85) cc_final: 0.7157 (tpt170) REVERT: A 561 ARG cc_start: 0.8315 (ptt180) cc_final: 0.8032 (mmt180) REVERT: A 631 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7500 (ttm-80) REVERT: A 717 THR cc_start: 0.8053 (m) cc_final: 0.7824 (p) REVERT: A 776 GLN cc_start: 0.8848 (mt0) cc_final: 0.8628 (tp40) REVERT: B 217 GLU cc_start: 0.8732 (pt0) cc_final: 0.8507 (pt0) REVERT: B 293 MET cc_start: 0.7393 (tpp) cc_final: 0.7167 (tpp) REVERT: B 361 HIS cc_start: 0.8068 (m-70) cc_final: 0.6717 (m-70) REVERT: B 403 MET cc_start: 0.7641 (tpp) cc_final: 0.7220 (tpp) REVERT: B 430 MET cc_start: 0.2598 (mmm) cc_final: 0.1896 (ttm) REVERT: B 606 PRO cc_start: 0.8703 (Cg_exo) cc_final: 0.8262 (Cg_endo) REVERT: B 629 MET cc_start: 0.8643 (ppp) cc_final: 0.8177 (ppp) REVERT: B 633 ASP cc_start: 0.7994 (p0) cc_final: 0.7308 (p0) REVERT: B 846 LEU cc_start: 0.9508 (mt) cc_final: 0.9115 (tt) REVERT: C 257 GLU cc_start: 0.8570 (tt0) cc_final: 0.8012 (tm-30) REVERT: C 595 ASN cc_start: 0.6076 (p0) cc_final: 0.5790 (p0) REVERT: C 615 CYS cc_start: 0.8831 (m) cc_final: 0.8353 (t) REVERT: C 827 ASN cc_start: 0.9097 (m-40) cc_final: 0.8638 (m-40) REVERT: D 232 LEU cc_start: 0.8365 (mt) cc_final: 0.8132 (mt) REVERT: D 524 MET cc_start: 0.5326 (mmm) cc_final: 0.4184 (mmt) REVERT: D 675 LEU cc_start: 0.8659 (tt) cc_final: 0.8438 (tp) REVERT: E 350 LEU cc_start: 0.9064 (mm) cc_final: 0.8748 (tp) REVERT: E 475 ILE cc_start: 0.8178 (pt) cc_final: 0.7831 (pt) REVERT: E 517 THR cc_start: 0.7443 (m) cc_final: 0.7194 (p) REVERT: E 552 MET cc_start: 0.7435 (pmm) cc_final: 0.6875 (pmm) REVERT: E 562 MET cc_start: 0.7755 (tpp) cc_final: 0.7453 (tpp) REVERT: E 616 LYS cc_start: 0.9381 (tppt) cc_final: 0.8927 (tppt) REVERT: E 638 MET cc_start: 0.8380 (pmm) cc_final: 0.7557 (ptp) REVERT: E 687 PHE cc_start: 0.8336 (m-10) cc_final: 0.7890 (m-80) REVERT: F 330 GLU cc_start: 0.7842 (tm-30) cc_final: 0.6762 (tp30) REVERT: F 401 ILE cc_start: 0.8455 (mm) cc_final: 0.8088 (mm) REVERT: F 498 MET cc_start: 0.6477 (tpp) cc_final: 0.5975 (tpp) REVERT: F 629 MET cc_start: 0.8442 (ppp) cc_final: 0.8005 (ppp) REVERT: F 684 PRO cc_start: 0.6360 (Cg_exo) cc_final: 0.6137 (Cg_endo) REVERT: F 737 MET cc_start: 0.8491 (mmm) cc_final: 0.7952 (mmm) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.1996 time to fit residues: 169.0303 Evaluate side-chains 367 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 267 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 93 optimal weight: 30.0000 chunk 319 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 107 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 770 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS C 334 GLN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.124539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.101043 restraints weight = 113280.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.102111 restraints weight = 76573.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.102305 restraints weight = 50748.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.102604 restraints weight = 48652.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.102668 restraints weight = 44945.436| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33304 Z= 0.130 Angle : 0.704 18.661 44929 Z= 0.344 Chirality : 0.043 0.245 5088 Planarity : 0.005 0.064 5869 Dihedral : 8.631 114.030 4748 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4077 helix: 1.01 (0.11), residues: 2418 sheet: -1.82 (0.25), residues: 392 loop : -1.41 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 819 TYR 0.016 0.001 TYR F 656 PHE 0.023 0.002 PHE E 637 TRP 0.010 0.001 TRP B 462 HIS 0.006 0.001 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00273 (33285) covalent geometry : angle 0.70360 (44929) hydrogen bonds : bond 0.03873 ( 1838) hydrogen bonds : angle 4.87767 ( 5427) Misc. bond : bond 0.00463 ( 19) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8154 Ramachandran restraints generated. 4077 Oldfield, 0 Emsley, 4077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.4396 (tpp) cc_final: 0.3903 (mmt) REVERT: A 318 GLU cc_start: 0.7579 (mp0) cc_final: 0.6918 (mp0) REVERT: A 525 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7186 (ttt180) REVERT: A 561 ARG cc_start: 0.8223 (ptt180) cc_final: 0.8007 (mmt180) REVERT: A 631 ARG cc_start: 0.7845 (ttt180) cc_final: 0.7342 (ttm-80) REVERT: A 717 THR cc_start: 0.7879 (m) cc_final: 0.7622 (p) REVERT: A 776 GLN cc_start: 0.8848 (mt0) cc_final: 0.8646 (tp40) REVERT: B 361 HIS cc_start: 0.8538 (m-70) cc_final: 0.8086 (m-70) REVERT: B 403 MET cc_start: 0.7589 (tpp) cc_final: 0.7210 (tpp) REVERT: B 430 MET cc_start: 0.2709 (mmm) cc_final: 0.1928 (ttm) REVERT: B 606 PRO cc_start: 0.8675 (Cg_exo) cc_final: 0.8224 (Cg_endo) REVERT: B 629 MET cc_start: 0.8564 (ppp) cc_final: 0.8154 (ppp) REVERT: B 737 MET cc_start: 0.6000 (mmt) cc_final: 0.5726 (mmt) REVERT: B 846 LEU cc_start: 0.9464 (mt) cc_final: 0.9088 (tt) REVERT: C 257 GLU cc_start: 0.8353 (tt0) cc_final: 0.7867 (tm-30) REVERT: C 524 MET cc_start: 0.0047 (ttp) cc_final: -0.0286 (ttp) REVERT: C 581 SER cc_start: 0.8087 (m) cc_final: 0.7216 (p) REVERT: C 595 ASN cc_start: 0.5951 (p0) cc_final: 0.5660 (p0) REVERT: C 615 CYS cc_start: 0.8565 (m) cc_final: 0.8100 (t) REVERT: C 827 ASN cc_start: 0.8962 (m-40) cc_final: 0.8449 (m-40) REVERT: D 217 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7294 (mm-30) REVERT: D 316 LEU cc_start: 0.8848 (tp) cc_final: 0.8623 (tp) REVERT: D 389 LYS cc_start: 0.7600 (ptmm) cc_final: 0.7212 (pttp) REVERT: D 524 MET cc_start: 0.5409 (mmm) cc_final: 0.5093 (tpp) REVERT: E 443 MET cc_start: 0.6077 (tmm) cc_final: 0.3518 (mtt) REVERT: E 475 ILE cc_start: 0.8187 (pt) cc_final: 0.7850 (pt) REVERT: E 517 THR cc_start: 0.7325 (m) cc_final: 0.7083 (p) REVERT: E 552 MET cc_start: 0.7439 (pmm) cc_final: 0.6948 (pmm) REVERT: E 562 MET cc_start: 0.7499 (tpp) cc_final: 0.7238 (tpp) REVERT: E 642 SER cc_start: 0.8657 (m) cc_final: 0.8408 (m) REVERT: E 687 PHE cc_start: 0.8096 (m-10) cc_final: 0.7626 (m-80) REVERT: E 694 LEU cc_start: 0.8469 (mt) cc_final: 0.8101 (tt) REVERT: F 167 ASP cc_start: 0.7399 (t0) cc_final: 0.6730 (t0) REVERT: F 240 LEU cc_start: 0.7273 (tp) cc_final: 0.6702 (tt) REVERT: F 245 LEU cc_start: 0.5086 (mm) cc_final: 0.4845 (mm) REVERT: F 298 MET cc_start: 0.5662 (mmm) cc_final: 0.5144 (mmt) REVERT: F 330 GLU cc_start: 0.7807 (tm-30) cc_final: 0.6696 (tp30) REVERT: F 401 ILE cc_start: 0.8410 (mm) cc_final: 0.7377 (mm) REVERT: F 405 ILE cc_start: 0.6180 (mm) cc_final: 0.5871 (mm) REVERT: F 462 TRP cc_start: 0.7664 (t60) cc_final: 0.5910 (t60) REVERT: F 498 MET cc_start: 0.6558 (tpp) cc_final: 0.6028 (tpp) REVERT: F 629 MET cc_start: 0.8397 (ppp) cc_final: 0.7959 (ppp) REVERT: F 684 PRO cc_start: 0.6693 (Cg_exo) cc_final: 0.6423 (Cg_endo) REVERT: F 713 VAL cc_start: 0.7571 (t) cc_final: 0.7192 (t) REVERT: F 737 MET cc_start: 0.8364 (mmm) cc_final: 0.7876 (mmm) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.1939 time to fit residues: 174.2829 Evaluate side-chains 387 residues out of total 3446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 239 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 315 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 134 optimal weight: 0.5980 chunk 216 optimal weight: 0.0370 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.124254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.100763 restraints weight = 113181.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.102130 restraints weight = 76117.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.101936 restraints weight = 51646.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.102461 restraints weight = 51088.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.102596 restraints weight = 44625.536| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33304 Z= 0.135 Angle : 0.699 18.851 44929 Z= 0.342 Chirality : 0.043 0.246 5088 Planarity : 0.005 0.056 5869 Dihedral : 8.563 112.557 4748 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4077 helix: 1.03 (0.11), residues: 2425 sheet: -1.82 (0.24), residues: 405 loop : -1.39 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 819 TYR 0.015 0.001 TYR F 656 PHE 0.027 0.002 PHE E 637 TRP 0.008 0.001 TRP B 543 HIS 0.006 0.001 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00291 (33285) covalent geometry : angle 0.69901 (44929) hydrogen bonds : bond 0.03851 ( 1838) hydrogen bonds : angle 4.86202 ( 5427) Misc. bond : bond 0.00467 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5930.42 seconds wall clock time: 103 minutes 14.02 seconds (6194.02 seconds total)