Starting phenix.real_space_refine on Mon Aug 25 19:10:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmt_50567/08_2025/9fmt_50567.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmt_50567/08_2025/9fmt_50567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fmt_50567/08_2025/9fmt_50567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmt_50567/08_2025/9fmt_50567.map" model { file = "/net/cci-nas-00/data/ceres_data/9fmt_50567/08_2025/9fmt_50567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmt_50567/08_2025/9fmt_50567.cif" } resolution = 2.35 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 19165 2.51 5 N 5143 2.21 5 O 5694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30144 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5118 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 655, 5107 Classifications: {'peptide': 655} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 602} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 655, 5107 Classifications: {'peptide': 655} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 602} Chain breaks: 1 bond proxies already assigned to first conformer: 5217 Chain: "B" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5112 Classifications: {'peptide': 656} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 603} Chain breaks: 1 Chain: "D" Number of atoms: 5087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5087 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 600} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4924 Classifications: {'peptide': 631} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 582} Chain breaks: 2 Chain: "F" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5235 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 617} Chain: "C" Number of atoms: 4668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4668 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 550} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 647 " occ=0.44 ... (20 atoms not shown) pdb=" NH2BARG A 647 " occ=0.56 Time building chain proxies: 8.28, per 1000 atoms: 0.27 Number of scatterers: 30144 At special positions: 0 Unit cell: (138.435, 177.029, 174.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 5694 8.00 N 5143 7.00 C 19165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 500 " distance=2.03 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 500 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 500 " distance=2.03 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 500 " distance=2.03 Simple disulfide: pdb=" SG CYS F 182 " - pdb=" SG CYS F 500 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7208 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 65 sheets defined 20.9% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 240 through 258 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.823A pdb=" N ARG A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.832A pdb=" N LYS A 475 " --> pdb=" O PRO A 472 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 476 " --> pdb=" O ALA A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 476' Processing helix chain 'A' and resid 531 through 539 Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 560 through 579 Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.687A pdb=" N THR A 593 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 594 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 595 " --> pdb=" O SER A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 590 through 595' Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.913A pdb=" N ASP A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 697 Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 737 through 740 Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.539A pdb=" N LEU B 149 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.517A pdb=" N PHE B 163 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 259 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 321 through 336 removed outlier: 3.833A pdb=" N ASN B 336 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 472 through 476 removed outlier: 4.112A pdb=" N LYS B 475 " --> pdb=" O PRO B 472 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 476 " --> pdb=" O ALA B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 531 through 539 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 579 removed outlier: 3.800A pdb=" N ILE B 574 " --> pdb=" O THR B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 removed outlier: 3.879A pdb=" N ASP B 613 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 684 through 697 Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 731 through 740 removed outlier: 4.012A pdb=" N LEU B 740 " --> pdb=" O LEU B 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 321 through 336 removed outlier: 3.932A pdb=" N ASN D 336 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 531 through 539 Processing helix chain 'D' and resid 539 through 544 Processing helix chain 'D' and resid 560 through 579 Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.687A pdb=" N THR D 593 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE D 594 " --> pdb=" O GLY D 591 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN D 595 " --> pdb=" O SER D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 590 through 595' Processing helix chain 'D' and resid 608 through 613 removed outlier: 3.670A pdb=" N ASP D 613 " --> pdb=" O ASP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 647 Processing helix chain 'D' and resid 684 through 697 Processing helix chain 'D' and resid 697 through 703 removed outlier: 3.609A pdb=" N THR D 703 " --> pdb=" O GLY D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 738 removed outlier: 3.688A pdb=" N TRP D 737 " --> pdb=" O PHE D 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 212 through 216 removed outlier: 3.761A pdb=" N HIS E 215 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 259 Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 321 through 335 Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 531 through 539 Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 560 through 579 Processing helix chain 'E' and resid 590 through 594 removed outlier: 3.691A pdb=" N THR E 593 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE E 594 " --> pdb=" O GLY E 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 590 through 594' Processing helix chain 'E' and resid 684 through 697 Processing helix chain 'E' and resid 697 through 702 Processing helix chain 'E' and resid 731 through 736 Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.558A pdb=" N PHE F 163 " --> pdb=" O ASN F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.718A pdb=" N ARG F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 335 Processing helix chain 'F' and resid 448 through 453 removed outlier: 3.910A pdb=" N LEU F 453 " --> pdb=" O ALA F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 539 removed outlier: 3.638A pdb=" N PHE F 535 " --> pdb=" O ASP F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 544 Processing helix chain 'F' and resid 560 through 579 Processing helix chain 'F' and resid 590 through 595 removed outlier: 3.536A pdb=" N ILE F 594 " --> pdb=" O GLY F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 613 removed outlier: 4.223A pdb=" N ASP F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 648 Processing helix chain 'F' and resid 684 through 697 Processing helix chain 'F' and resid 697 through 702 Processing helix chain 'F' and resid 731 through 737 Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.572A pdb=" N LEU C 149 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.624A pdb=" N HIS C 215 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 258 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 373 through 376 Processing helix chain 'C' and resid 531 through 539 removed outlier: 3.802A pdb=" N PHE C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 544 Processing helix chain 'C' and resid 560 through 579 removed outlier: 3.693A pdb=" N LEU C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 697 Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 731 through 741 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.728A pdb=" N LYS A 110 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN A 205 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL A 108 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.728A pdb=" N LYS A 110 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN A 205 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL A 108 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 101 removed outlier: 6.604A pdb=" N LEU A 130 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL A 141 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 132 " --> pdb=" O MET A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 230 removed outlier: 6.235A pdb=" N ASN A 229 " --> pdb=" O ASN A 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 269 removed outlier: 6.906A pdb=" N ALA A 277 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 317 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 279 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY A 319 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 281 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL A 346 " --> pdb=" O THR D 656 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR D 656 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 348 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR D 651 " --> pdb=" O THR D 630 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP D 627 " --> pdb=" O LEU D 620 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 620 " --> pdb=" O TRP D 627 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 383 through 386 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 397 removed outlier: 5.790A pdb=" N LEU A 433 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 471 Processing sheet with id=AA9, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AB1, first strand: chain 'A' and resid 500 through 502 removed outlier: 5.482A pdb=" N CYS A 500 " --> pdb=" O GLY D 494 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 529 Processing sheet with id=AB3, first strand: chain 'A' and resid 586 through 588 removed outlier: 6.523A pdb=" N THR A 551 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR A 588 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR A 553 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 601 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU A 680 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 603 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ALA A 682 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 619 through 622 removed outlier: 3.874A pdb=" N THR A 651 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLU A 650 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG A 652 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 349 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR A 654 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 277 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL B 317 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 279 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLY B 319 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 281 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.981A pdb=" N LYS B 110 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN B 205 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL B 108 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 193 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.981A pdb=" N LYS B 110 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN B 205 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL B 108 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA B 111 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 95 through 101 removed outlier: 6.487A pdb=" N LEU B 130 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL B 141 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 132 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 230 removed outlier: 6.098A pdb=" N ASN B 229 " --> pdb=" O ASN B 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 370 through 371 Processing sheet with id=AC1, first strand: chain 'B' and resid 370 through 371 Processing sheet with id=AC2, first strand: chain 'B' and resid 392 through 397 removed outlier: 5.996A pdb=" N LEU B 433 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AC4, first strand: chain 'B' and resid 526 through 529 Processing sheet with id=AC5, first strand: chain 'B' and resid 586 through 588 removed outlier: 6.478A pdb=" N THR B 551 " --> pdb=" O THR B 586 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR B 588 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR B 553 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 601 " --> pdb=" O ILE B 678 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 680 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE B 603 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA B 682 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 708 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 619 through 621 removed outlier: 3.860A pdb=" N THR B 651 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 348 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 656 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL C 346 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HIS C 306 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL C 312 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 277 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET C 233 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 70 through 76 removed outlier: 6.875A pdb=" N GLY D 199 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU D 113 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP D 201 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA D 111 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR D 203 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 70 through 76 removed outlier: 6.875A pdb=" N GLY D 199 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU D 113 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP D 201 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA D 111 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR D 203 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D 111 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 95 through 101 removed outlier: 3.699A pdb=" N GLY D 140 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 134 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 229 through 230 removed outlier: 6.166A pdb=" N ASN D 229 " --> pdb=" O ASN D 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 267 through 269 removed outlier: 6.889A pdb=" N ALA D 277 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL D 317 " --> pdb=" O ALA D 277 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL D 279 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLY D 319 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA D 281 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL D 312 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL D 346 " --> pdb=" O THR E 656 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR E 656 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU D 348 " --> pdb=" O THR E 654 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER E 626 " --> pdb=" O LEU E 655 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TRP E 627 " --> pdb=" O LEU E 620 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU E 620 " --> pdb=" O TRP E 627 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 370 through 371 Processing sheet with id=AD4, first strand: chain 'D' and resid 370 through 371 Processing sheet with id=AD5, first strand: chain 'D' and resid 392 through 397 removed outlier: 5.992A pdb=" N LEU D 433 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE D 437 " --> pdb=" O LEU D 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 402 through 403 Processing sheet with id=AD7, first strand: chain 'D' and resid 500 through 502 removed outlier: 5.244A pdb=" N CYS D 500 " --> pdb=" O GLY E 494 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 586 through 588 removed outlier: 6.479A pdb=" N THR D 551 " --> pdb=" O THR D 586 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR D 588 " --> pdb=" O THR D 551 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR D 553 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE D 601 " --> pdb=" O ILE D 678 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU D 680 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE D 603 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA D 682 " --> pdb=" O ILE D 603 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 70 through 76 removed outlier: 3.837A pdb=" N LYS E 110 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN E 205 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL E 108 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 70 through 76 removed outlier: 3.837A pdb=" N LYS E 110 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN E 205 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL E 108 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 95 through 101 removed outlier: 3.588A pdb=" N GLY E 140 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU E 134 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU E 138 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 229 through 230 removed outlier: 6.232A pdb=" N ASN E 229 " --> pdb=" O ASN E 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 267 through 269 removed outlier: 6.817A pdb=" N ALA E 277 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL E 317 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL E 279 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY E 319 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA E 281 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL E 312 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL E 346 " --> pdb=" O THR F 656 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR F 656 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR F 630 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG F 652 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL F 628 " --> pdb=" O ARG F 652 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR F 654 " --> pdb=" O SER F 626 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER F 626 " --> pdb=" O THR F 654 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 370 through 371 Processing sheet with id=AE6, first strand: chain 'E' and resid 383 through 386 Processing sheet with id=AE7, first strand: chain 'E' and resid 392 through 397 removed outlier: 6.422A pdb=" N MET E 429 " --> pdb=" O SER E 440 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER E 440 " --> pdb=" O MET E 429 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE E 431 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 526 through 529 Processing sheet with id=AE9, first strand: chain 'E' and resid 586 through 588 removed outlier: 6.499A pdb=" N THR E 551 " --> pdb=" O THR E 586 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR E 588 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR E 553 " --> pdb=" O THR E 588 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE E 552 " --> pdb=" O MET E 602 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE E 604 " --> pdb=" O ILE E 552 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL E 554 " --> pdb=" O ILE E 604 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 601 " --> pdb=" O ILE E 678 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU E 680 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE E 603 " --> pdb=" O LEU E 680 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA E 682 " --> pdb=" O ILE E 603 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 70 through 76 removed outlier: 6.746A pdb=" N GLY F 199 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU F 113 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP F 201 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA F 111 " --> pdb=" O ASP F 201 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR F 203 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 70 through 76 removed outlier: 6.746A pdb=" N GLY F 199 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU F 113 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP F 201 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA F 111 " --> pdb=" O ASP F 201 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR F 203 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA F 111 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 95 through 101 removed outlier: 3.507A pdb=" N GLY F 140 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 229 through 230 removed outlier: 6.076A pdb=" N ASN F 229 " --> pdb=" O ASN F 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 267 through 269 removed outlier: 6.835A pdb=" N ALA F 277 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL F 317 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL F 279 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY F 319 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA F 281 " --> pdb=" O GLY F 319 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL F 312 " --> pdb=" O HIS F 306 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 370 through 371 removed outlier: 6.493A pdb=" N HIS F 509 " --> pdb=" O THR F 419 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 370 through 371 Processing sheet with id=AF8, first strand: chain 'F' and resid 392 through 397 removed outlier: 6.104A pdb=" N LEU F 433 " --> pdb=" O PHE F 437 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE F 437 " --> pdb=" O LEU F 433 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 402 through 403 Processing sheet with id=AG1, first strand: chain 'F' and resid 494 through 495 Processing sheet with id=AG2, first strand: chain 'F' and resid 586 through 588 removed outlier: 3.819A pdb=" N THR F 586 " --> pdb=" O THR F 551 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE F 601 " --> pdb=" O ILE F 678 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU F 680 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE F 603 " --> pdb=" O LEU F 680 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA F 682 " --> pdb=" O ILE F 603 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 70 through 74 removed outlier: 3.916A pdb=" N LYS C 110 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN C 205 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 108 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 70 through 74 removed outlier: 3.916A pdb=" N LYS C 110 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN C 205 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 108 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 95 through 101 removed outlier: 6.381A pdb=" N LEU C 130 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL C 141 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 132 " --> pdb=" O MET C 139 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 229 through 230 removed outlier: 6.308A pdb=" N ASN C 229 " --> pdb=" O ASN C 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'C' and resid 370 through 371 Processing sheet with id=AG8, first strand: chain 'C' and resid 370 through 371 Processing sheet with id=AG9, first strand: chain 'C' and resid 392 through 397 removed outlier: 3.610A pdb=" N GLN C 439 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU C 433 " --> pdb=" O PHE C 437 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 526 through 528 removed outlier: 3.796A pdb=" N ILE C 527 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 727 " --> pdb=" O ILE C 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'C' and resid 586 through 588 removed outlier: 3.532A pdb=" N THR C 586 " --> pdb=" O THR C 551 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 601 " --> pdb=" O ILE C 678 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU C 680 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 603 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA C 682 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY C 605 " --> pdb=" O ALA C 682 " (cutoff:3.500A) 1190 hydrogen bonds defined for protein. 3159 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: 8.33 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10037 1.34 - 1.46: 5996 1.46 - 1.58: 14555 1.58 - 1.69: 0 1.69 - 1.81: 272 Bond restraints: 30860 Sorted by residual: bond pdb=" C ILE C 527 " pdb=" N PRO C 528 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.12e-02 7.97e+03 1.31e+01 bond pdb=" CA PRO C 400 " pdb=" C PRO C 400 " ideal model delta sigma weight residual 1.528 1.511 0.017 1.20e-02 6.94e+03 1.91e+00 bond pdb=" CA ILE C 527 " pdb=" CB ILE C 527 " ideal model delta sigma weight residual 1.537 1.553 -0.016 1.29e-02 6.01e+03 1.54e+00 bond pdb=" CA VAL F 88 " pdb=" CB VAL F 88 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.07e+00 bond pdb=" C MET C 529 " pdb=" N PRO C 530 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.44e-01 ... (remaining 30855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 41134 1.30 - 2.61: 640 2.61 - 3.91: 205 3.91 - 5.22: 35 5.22 - 6.52: 4 Bond angle restraints: 42018 Sorted by residual: angle pdb=" N THR D 624 " pdb=" CA THR D 624 " pdb=" C THR D 624 " ideal model delta sigma weight residual 114.04 109.39 4.65 1.24e+00 6.50e-01 1.41e+01 angle pdb=" N PHE C 526 " pdb=" CA PHE C 526 " pdb=" C PHE C 526 " ideal model delta sigma weight residual 107.49 113.72 -6.23 1.74e+00 3.30e-01 1.28e+01 angle pdb=" C ASP A 643 " pdb=" CA ASP A 643 " pdb=" CB ASP A 643 " ideal model delta sigma weight residual 110.14 114.09 -3.95 1.60e+00 3.91e-01 6.08e+00 angle pdb=" C GLN C 79 " pdb=" N ILE C 80 " pdb=" CA ILE C 80 " ideal model delta sigma weight residual 121.97 126.24 -4.27 1.80e+00 3.09e-01 5.64e+00 angle pdb=" C SER B 187 " pdb=" N THR B 188 " pdb=" CA THR B 188 " ideal model delta sigma weight residual 121.54 125.95 -4.41 1.91e+00 2.74e-01 5.33e+00 ... (remaining 42013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 16532 17.86 - 35.73: 1714 35.73 - 53.59: 401 53.59 - 71.45: 59 71.45 - 89.32: 31 Dihedral angle restraints: 18737 sinusoidal: 7566 harmonic: 11171 Sorted by residual: dihedral pdb=" CB CYS F 182 " pdb=" SG CYS F 182 " pdb=" SG CYS F 500 " pdb=" CB CYS F 500 " ideal model delta sinusoidal sigma weight residual -86.00 -146.41 60.41 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CA LEU B 213 " pdb=" C LEU B 213 " pdb=" N SER B 214 " pdb=" CA SER B 214 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU A 213 " pdb=" C LEU A 213 " pdb=" N SER A 214 " pdb=" CA SER A 214 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 18734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3773 0.052 - 0.104: 727 0.104 - 0.157: 185 0.157 - 0.209: 0 0.209 - 0.261: 1 Chirality restraints: 4686 Sorted by residual: chirality pdb=" CB ILE C 80 " pdb=" CA ILE C 80 " pdb=" CG1 ILE C 80 " pdb=" CG2 ILE C 80 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE C 527 " pdb=" N ILE C 527 " pdb=" C ILE C 527 " pdb=" CB ILE C 527 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE B 512 " pdb=" N ILE B 512 " pdb=" C ILE B 512 " pdb=" CB ILE B 512 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 4683 not shown) Planarity restraints: 5563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 81 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO B 82 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 82 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO A 83 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 368 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 369 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " 0.027 5.00e-02 4.00e+02 ... (remaining 5560 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 352 2.65 - 3.21: 25977 3.21 - 3.78: 45758 3.78 - 4.34: 66759 4.34 - 4.90: 109071 Nonbonded interactions: 247917 Sorted by model distance: nonbonded pdb=" OG SER C 676 " pdb=" OH TYR C 725 " model vdw 2.088 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" OG SER B 214 " model vdw 2.155 3.040 nonbonded pdb=" O ILE A 414 " pdb=" OG1 THR A 467 " model vdw 2.155 3.040 nonbonded pdb=" ND2 ASN C 276 " pdb=" O VAL C 312 " model vdw 2.166 3.120 nonbonded pdb=" OH TYR A 358 " pdb=" OD2 ASP A 401 " model vdw 2.196 3.040 ... (remaining 247912 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' and (resid 67 through 444 or resid 465 through 493 or resid 500 throu \ gh 606 or resid 659 through 737)) selection = (chain 'B' and (resid 67 through 444 or resid 465 through 493 or resid 500 throu \ gh 606 or resid 659 through 737)) selection = (chain 'C' and (resid 67 through 444 or resid 465 through 737)) selection = (chain 'D' and (resid 67 through 444 or resid 465 through 493 or resid 500 throu \ gh 606 or resid 659 through 737)) selection = (chain 'E' and (resid 67 through 493 or resid 500 through 606 or resid 659 throu \ gh 737)) selection = (chain 'F' and (resid 67 through 444 or resid 465 through 493 or resid 500 throu \ gh 606 or resid 659 through 737)) } 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=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.180 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.620 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.002 0.041 30865 Z= 0.112 Angle : 0.466 6.519 42028 Z= 0.243 Chirality : 0.044 0.261 4686 Planarity : 0.004 0.062 5563 Dihedral : 15.438 89.316 11514 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 0.90 % Allowed : 18.84 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.14), residues: 3839 helix: 1.74 (0.22), residues: 595 sheet: 1.67 (0.15), residues: 1188 loop : 0.18 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 428 TYR 0.014 0.001 TYR C 726 PHE 0.016 0.001 PHE A 573 TRP 0.011 0.001 TRP C 253 HIS 0.008 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00247 (30860) covalent geometry : angle 0.46603 (42018) SS BOND : bond 0.00284 ( 5) SS BOND : angle 0.53148 ( 10) hydrogen bonds : bond 0.16066 ( 1112) hydrogen bonds : angle 7.31455 ( 3159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 919 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8449 (tttt) cc_final: 0.8125 (mtpm) REVERT: A 646 ASP cc_start: 0.7255 (m-30) cc_final: 0.7011 (m-30) REVERT: D 92 ILE cc_start: 0.8560 (tp) cc_final: 0.8110 (tp) REVERT: D 380 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6610 (mm-30) REVERT: D 468 ASP cc_start: 0.7960 (m-30) cc_final: 0.7571 (m-30) REVERT: D 561 GLU cc_start: 0.8338 (mp0) cc_final: 0.8137 (mp0) REVERT: E 403 TYR cc_start: 0.8108 (t80) cc_final: 0.7546 (t80) REVERT: E 504 GLN cc_start: 0.8191 (tp40) cc_final: 0.7920 (tp40) REVERT: F 183 GLU cc_start: 0.8056 (tt0) cc_final: 0.7753 (tt0) REVERT: F 403 TYR cc_start: 0.8279 (t80) cc_final: 0.7993 (t80) REVERT: F 413 ASP cc_start: 0.7701 (t0) cc_final: 0.7412 (t0) REVERT: C 359 ASP cc_start: 0.7923 (p0) cc_final: 0.7679 (p0) REVERT: C 529 MET cc_start: 0.4872 (ttm) cc_final: 0.4625 (ttm) REVERT: C 560 ASN cc_start: 0.7700 (t0) cc_final: 0.7350 (t0) REVERT: C 561 GLU cc_start: 0.8010 (mp0) cc_final: 0.7390 (mp0) REVERT: C 597 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8113 (mtmt) REVERT: C 598 ASP cc_start: 0.7373 (t0) cc_final: 0.7161 (t0) REVERT: C 727 VAL cc_start: 0.8343 (m) cc_final: 0.8026 (t) REVERT: C 733 PHE cc_start: 0.8310 (p90) cc_final: 0.8075 (p90) outliers start: 30 outliers final: 18 residues processed: 946 average time/residue: 0.7713 time to fit residues: 845.6427 Evaluate side-chains 871 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 853 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 737 TRP Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 500 CYS Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 721 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 93 ASN A 114 ASN A 226 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 305 ASN B 362 ASN B 569 ASN B 696 ASN D 93 ASN D 156 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 481 GLN C 271 GLN C 334 GLN C 415 ASN C 504 GLN C 507 GLN C 717 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103804 restraints weight = 56707.998| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.93 r_work: 0.3376 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30865 Z= 0.213 Angle : 0.564 10.964 42028 Z= 0.294 Chirality : 0.049 0.277 4686 Planarity : 0.005 0.065 5563 Dihedral : 5.252 58.400 4183 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 3.01 % Allowed : 19.64 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.14), residues: 3839 helix: 1.66 (0.22), residues: 588 sheet: 1.57 (0.15), residues: 1156 loop : 0.10 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 735 TYR 0.016 0.002 TYR E 523 PHE 0.022 0.002 PHE A 573 TRP 0.014 0.001 TRP D 732 HIS 0.010 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00502 (30860) covalent geometry : angle 0.56344 (42018) SS BOND : bond 0.00626 ( 5) SS BOND : angle 0.94967 ( 10) hydrogen bonds : bond 0.04026 ( 1112) hydrogen bonds : angle 5.76166 ( 3159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 857 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8664 (tttt) cc_final: 0.8130 (mtpp) REVERT: A 365 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8200 (ptp-170) REVERT: A 368 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7676 (mtt180) REVERT: A 428 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8510 (ptt-90) REVERT: A 646 ASP cc_start: 0.7638 (m-30) cc_final: 0.7417 (m-30) REVERT: B 99 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7547 (mm-30) REVERT: D 573 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8590 (p90) REVERT: E 167 PHE cc_start: 0.7983 (t80) cc_final: 0.7725 (t80) REVERT: E 403 TYR cc_start: 0.8558 (t80) cc_final: 0.7884 (t80) REVERT: E 492 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7960 (mpp) REVERT: E 504 GLN cc_start: 0.8330 (tp40) cc_final: 0.8076 (tp40) REVERT: E 696 ASN cc_start: 0.8132 (p0) cc_final: 0.7829 (p0) REVERT: F 137 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7581 (tt0) REVERT: F 224 ARG cc_start: 0.8695 (mtt90) cc_final: 0.8428 (mtm-85) REVERT: F 405 MET cc_start: 0.7245 (mmm) cc_final: 0.6769 (mmm) REVERT: F 561 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: F 592 SER cc_start: 0.8771 (p) cc_final: 0.8531 (p) REVERT: C 359 ASP cc_start: 0.7921 (p0) cc_final: 0.7662 (p0) outliers start: 101 outliers final: 51 residues processed: 900 average time/residue: 0.8007 time to fit residues: 834.4831 Evaluate side-chains 890 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 834 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 737 TRP Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 500 CYS Chi-restraints excluded: chain F residue 531 ASP Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 502 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 133 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 378 optimal weight: 2.9990 chunk 347 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 160 ASN A 226 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN B 156 GLN B 215 HIS B 305 ASN D 93 ASN D 156 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN D 507 GLN E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 GLN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 ASN F 481 GLN C 271 GLN C 276 ASN C 334 GLN C 415 ASN C 507 GLN C 560 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103605 restraints weight = 59119.324| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.97 r_work: 0.3369 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 30865 Z= 0.192 Angle : 0.545 8.902 42028 Z= 0.283 Chirality : 0.048 0.277 4686 Planarity : 0.005 0.065 5563 Dihedral : 5.184 55.446 4176 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 3.13 % Allowed : 20.57 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.13), residues: 3839 helix: 1.54 (0.21), residues: 602 sheet: 1.43 (0.15), residues: 1151 loop : 0.02 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 169 TYR 0.018 0.002 TYR A 403 PHE 0.021 0.002 PHE A 573 TRP 0.014 0.001 TRP D 732 HIS 0.010 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00453 (30860) covalent geometry : angle 0.54488 (42018) SS BOND : bond 0.00572 ( 5) SS BOND : angle 1.08865 ( 10) hydrogen bonds : bond 0.03771 ( 1112) hydrogen bonds : angle 5.56881 ( 3159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 850 time to evaluate : 1.252 Fit side-chains REVERT: A 350 LYS cc_start: 0.8641 (tttt) cc_final: 0.8095 (mtpp) REVERT: A 365 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8262 (ptp-170) REVERT: A 368 ARG cc_start: 0.7990 (mtt180) cc_final: 0.7671 (mtt180) REVERT: A 428 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8503 (ptt-90) REVERT: A 612 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7740 (mtmm) REVERT: B 99 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7561 (mm-30) REVERT: D 151 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8450 (mmtm) REVERT: D 403 TYR cc_start: 0.8347 (t80) cc_final: 0.8031 (t80) REVERT: E 403 TYR cc_start: 0.8582 (t80) cc_final: 0.7889 (t80) REVERT: E 492 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7974 (mpp) REVERT: E 696 ASN cc_start: 0.8159 (p0) cc_final: 0.7922 (p0) REVERT: F 137 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7584 (tt0) REVERT: F 309 ASN cc_start: 0.8150 (t0) cc_final: 0.7902 (t0) REVERT: F 403 TYR cc_start: 0.8654 (t80) cc_final: 0.8226 (t80) REVERT: F 405 MET cc_start: 0.7495 (mmm) cc_final: 0.7009 (mmm) REVERT: F 561 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: F 592 SER cc_start: 0.8785 (p) cc_final: 0.8551 (p) REVERT: F 693 ASP cc_start: 0.7953 (t0) cc_final: 0.7680 (t0) REVERT: F 700 LYS cc_start: 0.8669 (mttt) cc_final: 0.8464 (mtmt) REVERT: C 527 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6982 (mt) REVERT: C 727 VAL cc_start: 0.8154 (m) cc_final: 0.7818 (t) outliers start: 105 outliers final: 56 residues processed: 892 average time/residue: 0.8096 time to fit residues: 835.8350 Evaluate side-chains 892 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 830 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 693 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 500 CYS Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 721 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 373 optimal weight: 0.4980 chunk 139 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 243 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.0020 chunk 222 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 160 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 305 ASN B 504 GLN D 156 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN D 507 GLN E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN F 442 ASN F 481 GLN C 271 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 504 GLN C 507 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.118508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103603 restraints weight = 64534.099| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.07 r_work: 0.3367 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30865 Z= 0.154 Angle : 0.526 8.525 42028 Z= 0.273 Chirality : 0.047 0.272 4686 Planarity : 0.005 0.063 5563 Dihedral : 4.936 52.348 4169 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.13 % Rotamer: Outliers : 3.13 % Allowed : 20.90 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.13), residues: 3839 helix: 1.65 (0.21), residues: 596 sheet: 1.35 (0.15), residues: 1156 loop : 0.04 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 169 TYR 0.021 0.001 TYR E 523 PHE 0.018 0.001 PHE B 573 TRP 0.012 0.001 TRP D 732 HIS 0.009 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00360 (30860) covalent geometry : angle 0.52632 (42018) SS BOND : bond 0.00603 ( 5) SS BOND : angle 1.00402 ( 10) hydrogen bonds : bond 0.03411 ( 1112) hydrogen bonds : angle 5.42743 ( 3159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 842 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8652 (tttt) cc_final: 0.8099 (mtpp) REVERT: A 365 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8268 (ptp-170) REVERT: A 368 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7625 (mtt180) REVERT: A 428 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8469 (ptt-90) REVERT: A 612 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7855 (mtmm) REVERT: A 732 TRP cc_start: 0.7401 (p-90) cc_final: 0.7095 (p-90) REVERT: B 224 ARG cc_start: 0.8419 (mtm180) cc_final: 0.8194 (mtm-85) REVERT: D 403 TYR cc_start: 0.8326 (t80) cc_final: 0.8082 (t80) REVERT: D 573 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8567 (p90) REVERT: D 737 TRP cc_start: 0.6122 (OUTLIER) cc_final: 0.5701 (t60) REVERT: E 403 TYR cc_start: 0.8605 (t80) cc_final: 0.7940 (t80) REVERT: E 696 ASN cc_start: 0.8188 (p0) cc_final: 0.7980 (p0) REVERT: F 224 ARG cc_start: 0.8654 (mtt90) cc_final: 0.8426 (mtm-85) REVERT: F 309 ASN cc_start: 0.8125 (t0) cc_final: 0.7897 (t0) REVERT: F 403 TYR cc_start: 0.8685 (t80) cc_final: 0.8329 (t80) REVERT: F 405 MET cc_start: 0.7421 (mmm) cc_final: 0.7010 (mmm) REVERT: F 592 SER cc_start: 0.8788 (p) cc_final: 0.8559 (p) REVERT: F 693 ASP cc_start: 0.8005 (t0) cc_final: 0.7739 (t0) REVERT: F 700 LYS cc_start: 0.8702 (mttt) cc_final: 0.8473 (mtmm) REVERT: C 527 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7121 (mt) REVERT: C 733 PHE cc_start: 0.8434 (p90) cc_final: 0.8139 (p90) outliers start: 105 outliers final: 59 residues processed: 888 average time/residue: 0.6693 time to fit residues: 689.0536 Evaluate side-chains 888 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 824 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 737 TRP Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 415 ASN Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 721 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 160 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 353 optimal weight: 0.7980 chunk 332 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 349 optimal weight: 0.2980 chunk 237 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 305 ASN B 504 GLN D 156 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN C 276 ASN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 442 ASN C 507 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.102139 restraints weight = 64847.263| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.08 r_work: 0.3342 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 30865 Z= 0.260 Angle : 0.581 9.345 42028 Z= 0.301 Chirality : 0.050 0.280 4686 Planarity : 0.005 0.066 5563 Dihedral : 5.124 51.177 4168 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 3.34 % Allowed : 20.63 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.13), residues: 3839 helix: 1.50 (0.22), residues: 584 sheet: 1.29 (0.15), residues: 1152 loop : -0.03 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 169 TYR 0.017 0.002 TYR A 403 PHE 0.020 0.002 PHE E 573 TRP 0.014 0.001 TRP D 732 HIS 0.012 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00620 (30860) covalent geometry : angle 0.58090 (42018) SS BOND : bond 0.00683 ( 5) SS BOND : angle 1.01923 ( 10) hydrogen bonds : bond 0.03810 ( 1112) hydrogen bonds : angle 5.52457 ( 3159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 836 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 365 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8266 (ptp-170) REVERT: A 368 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7742 (mtt180) REVERT: A 428 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8545 (ptt-90) REVERT: A 612 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7921 (mtmm) REVERT: B 99 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 224 ARG cc_start: 0.8401 (mtm180) cc_final: 0.8181 (mtm-85) REVERT: D 92 ILE cc_start: 0.8477 (tt) cc_final: 0.8177 (tt) REVERT: D 151 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (mmtm) REVERT: D 403 TYR cc_start: 0.8356 (t80) cc_final: 0.8076 (t80) REVERT: D 592 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8404 (p) REVERT: E 696 ASN cc_start: 0.8221 (p0) cc_final: 0.7989 (p0) REVERT: F 309 ASN cc_start: 0.8177 (t0) cc_final: 0.7930 (t0) REVERT: F 405 MET cc_start: 0.7503 (mmm) cc_final: 0.7214 (mmm) REVERT: F 592 SER cc_start: 0.8815 (p) cc_final: 0.8546 (p) REVERT: F 693 ASP cc_start: 0.7989 (t0) cc_final: 0.7725 (t0) REVERT: F 700 LYS cc_start: 0.8727 (mttt) cc_final: 0.8502 (mtmm) REVERT: C 356 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8320 (mmmm) REVERT: C 527 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7466 (mt) REVERT: C 733 PHE cc_start: 0.8463 (p90) cc_final: 0.8173 (p90) outliers start: 112 outliers final: 67 residues processed: 883 average time/residue: 0.7235 time to fit residues: 739.8397 Evaluate side-chains 903 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 830 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 693 ASP Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 721 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 372 optimal weight: 0.7980 chunk 235 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 197 optimal weight: 0.0060 chunk 100 optimal weight: 0.0170 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 305 ASN B 504 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN F 481 GLN C 263 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 504 GLN C 507 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104001 restraints weight = 64720.982| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.09 r_work: 0.3368 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30865 Z= 0.140 Angle : 0.531 9.290 42028 Z= 0.275 Chirality : 0.047 0.271 4686 Planarity : 0.005 0.072 5563 Dihedral : 4.939 51.375 4166 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 2.72 % Allowed : 21.58 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.13), residues: 3839 helix: 1.52 (0.21), residues: 608 sheet: 1.25 (0.15), residues: 1152 loop : -0.01 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 169 TYR 0.025 0.001 TYR E 523 PHE 0.022 0.001 PHE B 573 TRP 0.012 0.001 TRP D 732 HIS 0.010 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00324 (30860) covalent geometry : angle 0.53071 (42018) SS BOND : bond 0.00475 ( 5) SS BOND : angle 0.74373 ( 10) hydrogen bonds : bond 0.03302 ( 1112) hydrogen bonds : angle 5.35414 ( 3159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 846 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 365 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8274 (ptp-170) REVERT: A 368 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7710 (mtt180) REVERT: A 428 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8490 (ptt-90) REVERT: A 612 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7852 (mtmm) REVERT: A 693 ASP cc_start: 0.7979 (t70) cc_final: 0.7769 (t70) REVERT: D 151 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8484 (mmtm) REVERT: D 592 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8357 (p) REVERT: E 696 ASN cc_start: 0.8228 (p0) cc_final: 0.8026 (p0) REVERT: F 224 ARG cc_start: 0.8691 (mtt90) cc_final: 0.8152 (mtt90) REVERT: F 309 ASN cc_start: 0.8175 (t0) cc_final: 0.7940 (t0) REVERT: F 405 MET cc_start: 0.7379 (mmm) cc_final: 0.7140 (mmm) REVERT: F 592 SER cc_start: 0.8832 (p) cc_final: 0.8585 (p) REVERT: F 693 ASP cc_start: 0.7972 (t0) cc_final: 0.7665 (t0) REVERT: F 700 LYS cc_start: 0.8718 (mttt) cc_final: 0.8460 (mtmm) REVERT: C 524 TYR cc_start: 0.8381 (m-80) cc_final: 0.7834 (m-80) REVERT: C 527 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7385 (mt) REVERT: C 733 PHE cc_start: 0.8412 (p90) cc_final: 0.8149 (p90) outliers start: 91 outliers final: 58 residues processed: 883 average time/residue: 0.7602 time to fit residues: 776.5810 Evaluate side-chains 894 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 831 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 415 ASN Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 721 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 52 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 246 optimal weight: 0.0060 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 160 ASN A 436 GLN A 537 ASN B 156 GLN B 305 ASN D 156 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 481 GLN C 276 ASN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 442 ASN C 507 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.116696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102708 restraints weight = 53156.721| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.84 r_work: 0.3395 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30865 Z= 0.139 Angle : 0.530 8.485 42028 Z= 0.273 Chirality : 0.047 0.269 4686 Planarity : 0.005 0.075 5563 Dihedral : 4.881 52.277 4166 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 2.99 % Allowed : 22.12 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.13), residues: 3839 helix: 1.49 (0.21), residues: 620 sheet: 1.24 (0.15), residues: 1152 loop : 0.02 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 169 TYR 0.011 0.001 TYR D 523 PHE 0.021 0.001 PHE B 573 TRP 0.012 0.001 TRP D 732 HIS 0.009 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00325 (30860) covalent geometry : angle 0.52955 (42018) SS BOND : bond 0.00457 ( 5) SS BOND : angle 0.72634 ( 10) hydrogen bonds : bond 0.03243 ( 1112) hydrogen bonds : angle 5.28545 ( 3159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 844 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 365 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8266 (ptp-170) REVERT: A 368 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7647 (mtt180) REVERT: A 428 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8483 (ptt-90) REVERT: A 732 TRP cc_start: 0.7385 (p-90) cc_final: 0.7107 (p-90) REVERT: D 151 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8429 (mmtm) REVERT: D 403 TYR cc_start: 0.8302 (t80) cc_final: 0.8059 (t80) REVERT: D 592 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8342 (p) REVERT: E 696 ASN cc_start: 0.8188 (p0) cc_final: 0.7969 (p0) REVERT: F 224 ARG cc_start: 0.8672 (mtt90) cc_final: 0.8393 (mtt90) REVERT: F 309 ASN cc_start: 0.8141 (t0) cc_final: 0.7902 (t0) REVERT: F 592 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8579 (p) REVERT: F 693 ASP cc_start: 0.7894 (t0) cc_final: 0.7564 (t0) REVERT: F 700 LYS cc_start: 0.8690 (mttt) cc_final: 0.8410 (mtmm) REVERT: C 524 TYR cc_start: 0.8328 (m-80) cc_final: 0.7779 (m-80) REVERT: C 527 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7320 (mt) REVERT: C 733 PHE cc_start: 0.8388 (p90) cc_final: 0.8120 (p90) outliers start: 100 outliers final: 59 residues processed: 888 average time/residue: 0.6910 time to fit residues: 709.7901 Evaluate side-chains 909 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 844 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 285 LYS Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 ASN Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 721 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 238 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 350 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 366 optimal weight: 0.7980 chunk 291 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 160 ASN A 226 ASN B 156 GLN B 305 ASN B 504 GLN D 156 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN C 263 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 507 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.103404 restraints weight = 64686.554| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.09 r_work: 0.3360 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30865 Z= 0.187 Angle : 0.554 7.937 42028 Z= 0.285 Chirality : 0.048 0.271 4686 Planarity : 0.005 0.082 5563 Dihedral : 4.970 51.792 4166 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 2.72 % Allowed : 22.51 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.13), residues: 3839 helix: 1.52 (0.22), residues: 602 sheet: 1.25 (0.15), residues: 1148 loop : -0.01 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 169 TYR 0.022 0.002 TYR E 523 PHE 0.019 0.002 PHE A 573 TRP 0.013 0.001 TRP D 732 HIS 0.010 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00443 (30860) covalent geometry : angle 0.55372 (42018) SS BOND : bond 0.00554 ( 5) SS BOND : angle 0.86456 ( 10) hydrogen bonds : bond 0.03429 ( 1112) hydrogen bonds : angle 5.33104 ( 3159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 839 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 365 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8282 (ptp-170) REVERT: A 368 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7722 (mtt180) REVERT: A 428 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8516 (ptt-90) REVERT: A 732 TRP cc_start: 0.7416 (p-90) cc_final: 0.7131 (p-90) REVERT: D 151 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8480 (mmtm) REVERT: D 403 TYR cc_start: 0.8341 (t80) cc_final: 0.8017 (t80) REVERT: D 405 MET cc_start: 0.6569 (mmm) cc_final: 0.6111 (mmm) REVERT: D 592 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8358 (p) REVERT: E 696 ASN cc_start: 0.8247 (p0) cc_final: 0.8018 (p0) REVERT: F 224 ARG cc_start: 0.8716 (mtt90) cc_final: 0.8179 (mtt90) REVERT: F 309 ASN cc_start: 0.8201 (t0) cc_final: 0.7957 (t0) REVERT: F 405 MET cc_start: 0.7198 (mmm) cc_final: 0.6971 (mmm) REVERT: F 592 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8604 (p) REVERT: F 693 ASP cc_start: 0.7968 (t0) cc_final: 0.7755 (t0) REVERT: C 524 TYR cc_start: 0.8393 (m-80) cc_final: 0.7848 (m-80) REVERT: C 527 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7455 (mt) REVERT: C 733 PHE cc_start: 0.8413 (p90) cc_final: 0.8138 (p90) outliers start: 91 outliers final: 65 residues processed: 880 average time/residue: 0.7676 time to fit residues: 779.9490 Evaluate side-chains 900 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 829 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 ASN Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 721 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 174 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 240 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 252 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 173 optimal weight: 0.9990 chunk 285 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 293 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 160 ASN A 226 ASN B 156 GLN B 305 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN F 481 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 507 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.102105 restraints weight = 57333.305| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.93 r_work: 0.3384 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30865 Z= 0.155 Angle : 0.545 10.296 42028 Z= 0.281 Chirality : 0.047 0.267 4686 Planarity : 0.005 0.062 5563 Dihedral : 4.943 52.148 4166 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 2.69 % Allowed : 22.66 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.13), residues: 3839 helix: 1.48 (0.21), residues: 614 sheet: 1.23 (0.15), residues: 1136 loop : 0.01 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 735 TYR 0.013 0.001 TYR E 488 PHE 0.019 0.001 PHE B 573 TRP 0.012 0.001 TRP D 732 HIS 0.010 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00365 (30860) covalent geometry : angle 0.54493 (42018) SS BOND : bond 0.00507 ( 5) SS BOND : angle 0.77470 ( 10) hydrogen bonds : bond 0.03292 ( 1112) hydrogen bonds : angle 5.28842 ( 3159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 839 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 365 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8272 (ptp-170) REVERT: A 368 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7686 (mtt180) REVERT: A 428 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8487 (ptt-90) REVERT: A 732 TRP cc_start: 0.7403 (p-90) cc_final: 0.7113 (p-90) REVERT: A 735 ARG cc_start: 0.7871 (tpp80) cc_final: 0.7241 (ttt-90) REVERT: B 99 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7462 (mm-30) REVERT: D 151 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8467 (mmtm) REVERT: D 592 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8321 (p) REVERT: E 424 LYS cc_start: 0.8385 (mmtm) cc_final: 0.8132 (mmtm) REVERT: E 696 ASN cc_start: 0.8210 (p0) cc_final: 0.7983 (p0) REVERT: F 224 ARG cc_start: 0.8691 (mtt90) cc_final: 0.8113 (mtt90) REVERT: F 309 ASN cc_start: 0.8173 (t0) cc_final: 0.7934 (t0) REVERT: F 592 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8604 (p) REVERT: F 693 ASP cc_start: 0.7927 (t0) cc_final: 0.7717 (t0) REVERT: C 412 MET cc_start: 0.7790 (ttp) cc_final: 0.7489 (ttm) REVERT: C 524 TYR cc_start: 0.8360 (m-80) cc_final: 0.7863 (m-80) REVERT: C 527 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7402 (mt) REVERT: C 733 PHE cc_start: 0.8413 (p90) cc_final: 0.8168 (p90) outliers start: 90 outliers final: 65 residues processed: 878 average time/residue: 0.7731 time to fit residues: 784.7763 Evaluate side-chains 902 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 831 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 415 ASN Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 ASN Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 721 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 30 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 358 optimal weight: 0.0060 chunk 364 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 305 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 321 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 289 optimal weight: 0.3980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 160 ASN A 226 ASN B 305 ASN B 504 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 ASN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN C 276 ASN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 507 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.118642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.105189 restraints weight = 44120.531| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.66 r_work: 0.3411 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30865 Z= 0.150 Angle : 0.551 9.840 42028 Z= 0.283 Chirality : 0.047 0.265 4686 Planarity : 0.005 0.089 5563 Dihedral : 4.938 52.334 4166 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.39 % Allowed : 23.16 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.13), residues: 3839 helix: 1.50 (0.21), residues: 614 sheet: 1.22 (0.15), residues: 1136 loop : 0.02 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 169 TYR 0.023 0.001 TYR F 403 PHE 0.019 0.001 PHE B 573 TRP 0.012 0.001 TRP D 732 HIS 0.009 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00352 (30860) covalent geometry : angle 0.55118 (42018) SS BOND : bond 0.00484 ( 5) SS BOND : angle 0.77828 ( 10) hydrogen bonds : bond 0.03270 ( 1112) hydrogen bonds : angle 5.27908 ( 3159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 844 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8297 (mtt90) cc_final: 0.8067 (mtt90) REVERT: A 365 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8235 (ptp-170) REVERT: A 368 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7599 (mtt180) REVERT: A 428 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8455 (ptt-90) REVERT: A 732 TRP cc_start: 0.7374 (p-90) cc_final: 0.7083 (p-90) REVERT: A 735 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7183 (ttt-90) REVERT: B 99 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 619 LEU cc_start: 0.8767 (tp) cc_final: 0.8527 (tt) REVERT: D 151 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8401 (mmtm) REVERT: D 592 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8289 (p) REVERT: E 424 LYS cc_start: 0.8337 (mmtm) cc_final: 0.8089 (mmtm) REVERT: E 696 ASN cc_start: 0.8145 (p0) cc_final: 0.7924 (p0) REVERT: F 224 ARG cc_start: 0.8663 (mtt90) cc_final: 0.8095 (mtt90) REVERT: F 309 ASN cc_start: 0.8128 (t0) cc_final: 0.7899 (t0) REVERT: F 592 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8624 (p) REVERT: F 693 ASP cc_start: 0.7835 (t0) cc_final: 0.7633 (t0) REVERT: C 412 MET cc_start: 0.7620 (ttp) cc_final: 0.7329 (ttp) REVERT: C 524 TYR cc_start: 0.8311 (m-80) cc_final: 0.7808 (m-80) REVERT: C 527 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7366 (mt) REVERT: C 733 PHE cc_start: 0.8367 (p90) cc_final: 0.8121 (p90) outliers start: 80 outliers final: 63 residues processed: 879 average time/residue: 0.7038 time to fit residues: 718.0629 Evaluate side-chains 897 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 828 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 415 ASN Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 569 ASN Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 672 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 81 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 364 optimal weight: 0.0040 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 214 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 160 ASN A 226 ASN B 305 ASN B 504 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 GLN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 507 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.118506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104105 restraints weight = 57067.709| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.94 r_work: 0.3382 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30865 Z= 0.159 Angle : 0.554 10.744 42028 Z= 0.284 Chirality : 0.047 0.262 4686 Planarity : 0.005 0.062 5563 Dihedral : 4.949 52.271 4166 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 2.42 % Allowed : 23.16 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.13), residues: 3839 helix: 1.59 (0.22), residues: 596 sheet: 1.23 (0.15), residues: 1136 loop : -0.01 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 735 TYR 0.012 0.001 TYR A 403 PHE 0.019 0.002 PHE B 573 TRP 0.013 0.001 TRP D 732 HIS 0.009 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00376 (30860) covalent geometry : angle 0.55427 (42018) SS BOND : bond 0.00503 ( 5) SS BOND : angle 0.78393 ( 10) hydrogen bonds : bond 0.03294 ( 1112) hydrogen bonds : angle 5.27569 ( 3159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19401.48 seconds wall clock time: 328 minutes 51.15 seconds (19731.15 seconds total)