Starting phenix.real_space_refine on Thu Jun 26 02:34:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmt_50567/06_2025/9fmt_50567.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmt_50567/06_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_50567/06_2025/9fmt_50567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmt_50567/06_2025/9fmt_50567.map" model { file = "/net/cci-nas-00/data/ceres_data/9fmt_50567/06_2025/9fmt_50567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmt_50567/06_2025/9fmt_50567.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 24.12, per 1000 atoms: 0.80 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: 8.41 Conformation dependent library (CDL) restraints added in 5.0 seconds 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: 5.59 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: 15.38 Time building geometry restraints manager: 9.93 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: 8.110 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: 1.310 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 84.860 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.150 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:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (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 TRP 0.011 0.001 TRP C 253 HIS 0.008 0.001 HIS A 215 PHE 0.016 0.001 PHE A 573 TYR 0.014 0.001 TYR C 726 ARG 0.003 0.000 ARG E 428 Details of bonding type rmsd hydrogen bonds : bond 0.16066 ( 1112) hydrogen bonds : angle 7.31455 ( 3159) SS BOND : bond 0.00284 ( 5) SS BOND : angle 0.53148 ( 10) covalent geometry : bond 0.00247 (30860) covalent geometry : angle 0.46603 (42018) *********************** 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 : 3.462 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: 0.7349 (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: 1.8904 time to fit residues: 2074.4997 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 : 3.663 ------------------------------------------------------------------------------- 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 324 optimal weight: 2.9990 chunk 291 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 196 optimal weight: 0.0980 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 348 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** 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 = 0.3708 r_free = 0.3708 target = 0.119427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105264 restraints weight = 51543.265| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.82 r_work: 0.3401 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30865 Z= 0.153 Angle : 0.533 9.588 42028 Z= 0.278 Chirality : 0.047 0.273 4686 Planarity : 0.005 0.062 5563 Dihedral : 5.091 58.634 4183 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 2.51 % Allowed : 20.30 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3839 helix: 1.64 (0.22), residues: 602 sheet: 1.58 (0.15), residues: 1158 loop : 0.11 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 732 HIS 0.008 0.001 HIS A 215 PHE 0.020 0.002 PHE A 573 TYR 0.016 0.001 TYR E 523 ARG 0.013 0.001 ARG E 720 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 1112) hydrogen bonds : angle 5.76204 ( 3159) SS BOND : bond 0.00496 ( 5) SS BOND : angle 0.82811 ( 10) covalent geometry : bond 0.00354 (30860) covalent geometry : angle 0.53275 (42018) *********************** 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 944 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 860 time to evaluate : 3.245 Fit side-chains REVERT: A 350 LYS cc_start: 0.8627 (tttt) cc_final: 0.8131 (mtpp) REVERT: A 365 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8171 (ptp-170) REVERT: A 368 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7602 (mtt180) REVERT: A 428 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8470 (ptt-90) REVERT: A 646 ASP cc_start: 0.7534 (m-30) cc_final: 0.7291 (m-30) REVERT: D 573 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8552 (p90) REVERT: E 167 PHE cc_start: 0.7954 (t80) cc_final: 0.7685 (t80) REVERT: E 403 TYR cc_start: 0.8500 (t80) cc_final: 0.7820 (t80) REVERT: E 492 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7906 (mpp) REVERT: E 504 GLN cc_start: 0.8306 (tp40) cc_final: 0.8047 (tp40) REVERT: F 137 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7548 (tt0) REVERT: F 224 ARG cc_start: 0.8655 (mtt90) cc_final: 0.8407 (mtm-85) REVERT: F 405 MET cc_start: 0.7196 (mmm) cc_final: 0.6668 (mmm) REVERT: F 544 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7606 (ttp80) REVERT: F 592 SER cc_start: 0.8755 (p) cc_final: 0.8518 (p) REVERT: C 359 ASP cc_start: 0.7856 (p0) cc_final: 0.7600 (p0) outliers start: 84 outliers final: 42 residues processed: 897 average time/residue: 1.5725 time to fit residues: 1635.4357 Evaluate side-chains 879 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 832 time to evaluate : 3.187 ------------------------------------------------------------------------------- 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 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 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 658 SER 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 628 VAL 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 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 282 THR Chi-restraints excluded: chain F residue 450 ASN Chi-restraints excluded: chain F residue 500 CYS Chi-restraints excluded: chain F residue 544 ARG 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 C residue 141 VAL 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 215 optimal weight: 0.5980 chunk 272 optimal weight: 2.9990 chunk 378 optimal weight: 2.9990 chunk 50 optimal weight: 0.0370 chunk 22 optimal weight: 0.0770 chunk 261 optimal weight: 2.9990 chunk 375 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 273 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 305 ASN D 93 ASN D 156 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN ** 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 577 GLN E 595 GLN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 481 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.117656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103002 restraints weight = 62906.555| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.03 r_work: 0.3390 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 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 = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30865 Z= 0.123 Angle : 0.512 8.768 42028 Z= 0.265 Chirality : 0.046 0.269 4686 Planarity : 0.005 0.061 5563 Dihedral : 4.922 54.934 4175 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 2.93 % Allowed : 20.51 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3839 helix: 1.67 (0.21), residues: 614 sheet: 1.47 (0.15), residues: 1160 loop : 0.10 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 732 HIS 0.007 0.001 HIS A 215 PHE 0.017 0.001 PHE B 573 TYR 0.019 0.001 TYR F 403 ARG 0.010 0.000 ARG C 169 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 1112) hydrogen bonds : angle 5.45379 ( 3159) SS BOND : bond 0.00461 ( 5) SS BOND : angle 1.00870 ( 10) covalent geometry : bond 0.00280 (30860) covalent geometry : angle 0.51143 (42018) *********************** 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 960 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 862 time to evaluate : 4.629 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8644 (tttt) cc_final: 0.8211 (mtpm) REVERT: A 365 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8260 (ptp-170) REVERT: A 368 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7652 (mtt180) REVERT: A 428 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8451 (ptt-90) REVERT: A 646 ASP cc_start: 0.7666 (m-30) cc_final: 0.7443 (m-30) REVERT: B 99 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7427 (mm-30) REVERT: E 403 TYR cc_start: 0.8535 (t80) cc_final: 0.7858 (t80) REVERT: E 492 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7955 (mpp) REVERT: E 696 ASN cc_start: 0.8179 (p0) cc_final: 0.7946 (p0) REVERT: F 224 ARG cc_start: 0.8663 (mtt90) cc_final: 0.8443 (mtm-85) REVERT: F 309 ASN cc_start: 0.8099 (t0) cc_final: 0.7894 (t0) REVERT: F 403 TYR cc_start: 0.8640 (t80) cc_final: 0.8258 (t80) REVERT: F 404 LEU cc_start: 0.8849 (tp) cc_final: 0.8613 (tp) REVERT: F 405 MET cc_start: 0.7430 (mmm) cc_final: 0.6948 (mmm) REVERT: F 592 SER cc_start: 0.8767 (p) cc_final: 0.8539 (p) REVERT: C 197 SER cc_start: 0.8715 (p) cc_final: 0.8507 (t) REVERT: C 359 ASP cc_start: 0.7919 (p0) cc_final: 0.7649 (p0) REVERT: C 727 VAL cc_start: 0.7865 (m) cc_final: 0.7497 (t) outliers start: 98 outliers final: 54 residues processed: 902 average time/residue: 2.0934 time to fit residues: 2225.1090 Evaluate side-chains 891 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 834 time to evaluate : 3.772 ------------------------------------------------------------------------------- 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 573 PHE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 209 VAL 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 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 B residue 693 ASP Chi-restraints excluded: chain D residue 146 LYS 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 656 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 VAL 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 206 THR Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 415 ASN Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 500 CYS 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 621 VAL Chi-restraints excluded: chain F residue 644 GLU Chi-restraints excluded: chain C residue 385 SER 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 672 ASN Chi-restraints excluded: chain C residue 719 LEU 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 203 optimal weight: 1.9990 chunk 335 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 250 optimal weight: 1.9990 chunk 340 optimal weight: 0.0470 chunk 5 optimal weight: 0.1980 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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** 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 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 415 ASN E 595 GLN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN F 481 GLN C 271 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 442 ASN C 481 GLN C 504 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.117592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.103358 restraints weight = 56973.087| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.91 r_work: 0.3403 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30865 Z= 0.122 Angle : 0.510 9.100 42028 Z= 0.264 Chirality : 0.046 0.269 4686 Planarity : 0.005 0.061 5563 Dihedral : 4.731 52.927 4170 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 3.04 % Allowed : 20.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.13), residues: 3839 helix: 1.67 (0.21), residues: 620 sheet: 1.39 (0.15), residues: 1153 loop : 0.10 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 732 HIS 0.008 0.001 HIS A 215 PHE 0.018 0.001 PHE F 163 TYR 0.009 0.001 TYR D 523 ARG 0.012 0.000 ARG C 169 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 1112) hydrogen bonds : angle 5.31886 ( 3159) SS BOND : bond 0.00415 ( 5) SS BOND : angle 0.91156 ( 10) covalent geometry : bond 0.00281 (30860) covalent geometry : angle 0.51028 (42018) *********************** 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 960 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 858 time to evaluate : 3.245 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8631 (tttt) cc_final: 0.8131 (mtpp) REVERT: A 365 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8251 (ptp-170) REVERT: A 368 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7620 (mtt180) REVERT: A 428 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8459 (ptt-90) REVERT: A 504 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: B 99 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7379 (mm-30) REVERT: D 151 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8408 (mmtm) REVERT: D 737 TRP cc_start: 0.6051 (OUTLIER) cc_final: 0.5616 (t60) REVERT: E 403 TYR cc_start: 0.8541 (t80) cc_final: 0.7859 (t80) REVERT: E 696 ASN cc_start: 0.8175 (p0) cc_final: 0.7893 (p0) REVERT: F 224 ARG cc_start: 0.8662 (mtt90) cc_final: 0.8449 (mtm-85) REVERT: F 291 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7612 (mtm-85) REVERT: F 309 ASN cc_start: 0.8143 (t0) cc_final: 0.7926 (t0) REVERT: F 403 TYR cc_start: 0.8661 (t80) cc_final: 0.8268 (t80) REVERT: F 404 LEU cc_start: 0.8848 (tp) cc_final: 0.8606 (tp) REVERT: F 405 MET cc_start: 0.7394 (mmm) cc_final: 0.6989 (mmm) REVERT: F 544 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7584 (ttp80) REVERT: F 592 SER cc_start: 0.8794 (p) cc_final: 0.8582 (p) REVERT: C 436 GLN cc_start: 0.6577 (tt0) cc_final: 0.5703 (tt0) REVERT: C 524 TYR cc_start: 0.8306 (m-80) cc_final: 0.7719 (m-80) REVERT: C 527 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6742 (mt) REVERT: C 733 PHE cc_start: 0.8368 (p90) cc_final: 0.8108 (p90) outliers start: 102 outliers final: 58 residues processed: 904 average time/residue: 1.6370 time to fit residues: 1712.5426 Evaluate side-chains 906 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 841 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 152 LYS 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 504 GLN 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 A residue 678 ILE Chi-restraints excluded: chain B residue 92 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 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 B residue 693 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 151 LYS 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 67 ASN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 VAL 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 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 312 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 531 ASP Chi-restraints excluded: chain F residue 544 ARG 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 621 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 190 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 6 optimal weight: 1.9990 chunk 263 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 346 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 363 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 215 HIS 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 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 ASN C 271 GLN C 276 ASN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 481 GLN C 504 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104447 restraints weight = 55397.027| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.89 r_work: 0.3386 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30865 Z= 0.163 Angle : 0.529 9.409 42028 Z= 0.273 Chirality : 0.047 0.269 4686 Planarity : 0.005 0.062 5563 Dihedral : 4.792 52.447 4168 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 2.93 % Allowed : 21.58 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.13), residues: 3839 helix: 1.66 (0.21), residues: 608 sheet: 1.41 (0.15), residues: 1130 loop : 0.06 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 732 HIS 0.009 0.001 HIS B 215 PHE 0.028 0.002 PHE F 163 TYR 0.013 0.001 TYR A 403 ARG 0.013 0.000 ARG C 169 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 1112) hydrogen bonds : angle 5.32857 ( 3159) SS BOND : bond 0.00508 ( 5) SS BOND : angle 0.80767 ( 10) covalent geometry : bond 0.00384 (30860) covalent geometry : angle 0.52898 (42018) *********************** 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 946 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 848 time to evaluate : 3.715 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8632 (tttt) cc_final: 0.8124 (mtpp) REVERT: A 365 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8219 (ptp-170) REVERT: A 368 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7596 (mtt180) REVERT: A 428 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8458 (ptt-90) REVERT: A 612 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7658 (mtmm) REVERT: D 151 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8417 (mmtm) REVERT: D 573 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8526 (p90) REVERT: E 403 TYR cc_start: 0.8555 (t80) cc_final: 0.7879 (t80) REVERT: F 309 ASN cc_start: 0.8132 (t0) cc_final: 0.7912 (t0) REVERT: F 403 TYR cc_start: 0.8645 (t80) cc_final: 0.8243 (t80) REVERT: F 404 LEU cc_start: 0.8827 (tp) cc_final: 0.8580 (tp) REVERT: F 405 MET cc_start: 0.7474 (mmm) cc_final: 0.7165 (mmm) REVERT: F 592 SER cc_start: 0.8818 (p) cc_final: 0.8545 (p) REVERT: C 436 GLN cc_start: 0.6603 (tt0) cc_final: 0.5729 (tt0) REVERT: C 524 TYR cc_start: 0.8296 (m-80) cc_final: 0.7709 (m-80) REVERT: C 527 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6961 (mt) REVERT: C 733 PHE cc_start: 0.8370 (p90) cc_final: 0.8106 (p90) outliers start: 98 outliers final: 63 residues processed: 890 average time/residue: 1.6196 time to fit residues: 1669.7893 Evaluate side-chains 899 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 831 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 152 LYS 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 573 PHE 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 241 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 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 693 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 370 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 656 THR 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 241 VAL 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 147 GLU Chi-restraints excluded: chain F residue 152 LYS 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 312 VAL Chi-restraints excluded: chain F residue 415 ASN Chi-restraints excluded: chain F residue 447 GLN 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 621 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 325 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 6 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 289 optimal weight: 0.2980 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 A 383 GLN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 305 ASN D 156 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN C 271 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 442 ASN C 481 GLN C 507 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.115990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100983 restraints weight = 71025.781| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.16 r_work: 0.3353 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30865 Z= 0.186 Angle : 0.546 9.183 42028 Z= 0.282 Chirality : 0.048 0.273 4686 Planarity : 0.005 0.067 5563 Dihedral : 4.893 51.453 4166 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 3.46 % Allowed : 21.40 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 3839 helix: 1.52 (0.21), residues: 608 sheet: 1.34 (0.15), residues: 1147 loop : 0.05 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 732 HIS 0.009 0.002 HIS A 215 PHE 0.020 0.002 PHE E 167 TYR 0.016 0.001 TYR D 725 ARG 0.015 0.000 ARG C 169 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 1112) hydrogen bonds : angle 5.35795 ( 3159) SS BOND : bond 0.00574 ( 5) SS BOND : angle 0.86421 ( 10) covalent geometry : bond 0.00440 (30860) covalent geometry : angle 0.54555 (42018) *********************** 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 960 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 844 time to evaluate : 3.529 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8653 (tttt) cc_final: 0.8105 (mtpp) REVERT: A 365 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8289 (ptp-170) REVERT: A 368 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7656 (mtt180) REVERT: A 428 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8497 (ptt-90) REVERT: A 612 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7778 (mtmm) REVERT: D 151 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8473 (mmtm) REVERT: D 573 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8570 (p90) REVERT: D 592 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8356 (p) REVERT: F 224 ARG cc_start: 0.8701 (mtt90) cc_final: 0.8161 (mtt90) REVERT: F 309 ASN cc_start: 0.8182 (t0) cc_final: 0.7928 (t0) REVERT: F 404 LEU cc_start: 0.8852 (tp) cc_final: 0.8612 (tp) REVERT: F 405 MET cc_start: 0.7522 (mmm) cc_final: 0.7235 (mmm) REVERT: C 436 GLN cc_start: 0.6658 (tt0) cc_final: 0.5783 (tt0) REVERT: C 524 TYR cc_start: 0.8376 (m-80) cc_final: 0.7795 (m-80) REVERT: C 527 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7309 (mt) REVERT: C 733 PHE cc_start: 0.8422 (p90) cc_final: 0.8170 (p90) outliers start: 116 outliers final: 67 residues processed: 892 average time/residue: 1.6324 time to fit residues: 1700.1046 Evaluate side-chains 909 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 836 time to evaluate : 3.311 ------------------------------------------------------------------------------- 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 152 LYS 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 474 LEU 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 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 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 B residue 651 THR Chi-restraints excluded: chain B residue 693 ASP 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 370 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 E residue 67 ASN Chi-restraints excluded: chain E residue 152 LYS 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 207 LEU 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 338 LEU 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 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 325 LEU Chi-restraints excluded: chain C residue 395 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 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 151 optimal weight: 0.7980 chunk 244 optimal weight: 0.2980 chunk 308 optimal weight: 0.9990 chunk 373 optimal weight: 0.7980 chunk 355 optimal weight: 0.7980 chunk 177 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 323 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 383 GLN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 305 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102418 restraints weight = 55420.691| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.86 r_work: 0.3389 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30865 Z= 0.149 Angle : 0.533 9.384 42028 Z= 0.275 Chirality : 0.047 0.269 4686 Planarity : 0.005 0.076 5563 Dihedral : 4.847 51.599 4166 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 2.96 % Allowed : 22.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.13), residues: 3839 helix: 1.46 (0.21), residues: 620 sheet: 1.30 (0.15), residues: 1137 loop : 0.04 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 732 HIS 0.009 0.001 HIS A 215 PHE 0.018 0.001 PHE B 573 TYR 0.013 0.001 TYR D 725 ARG 0.017 0.000 ARG C 169 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 1112) hydrogen bonds : angle 5.29791 ( 3159) SS BOND : bond 0.00488 ( 5) SS BOND : angle 0.76272 ( 10) covalent geometry : bond 0.00351 (30860) covalent geometry : angle 0.53304 (42018) *********************** 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 938 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 839 time to evaluate : 3.294 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8629 (tttt) cc_final: 0.8427 (ttpt) REVERT: A 365 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8240 (ptp-170) REVERT: A 368 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7574 (mtt180) REVERT: A 428 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8455 (ptt-90) REVERT: A 693 ASP cc_start: 0.7873 (t70) cc_final: 0.7658 (t70) REVERT: B 99 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 318 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8405 (m-80) REVERT: D 151 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8426 (mmtm) REVERT: D 387 LEU cc_start: 0.8706 (mm) cc_final: 0.8503 (mp) REVERT: D 573 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8513 (p90) REVERT: D 592 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8328 (p) REVERT: F 224 ARG cc_start: 0.8666 (mtt90) cc_final: 0.8379 (mtt90) REVERT: F 309 ASN cc_start: 0.8118 (t0) cc_final: 0.7878 (t0) REVERT: C 436 GLN cc_start: 0.6599 (tt0) cc_final: 0.5805 (tt0) REVERT: C 524 TYR cc_start: 0.8307 (m-80) cc_final: 0.7760 (m-80) REVERT: C 527 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7284 (mt) REVERT: C 727 VAL cc_start: 0.8231 (m) cc_final: 0.7865 (t) REVERT: C 733 PHE cc_start: 0.8376 (p90) cc_final: 0.8138 (p90) outliers start: 99 outliers final: 64 residues processed: 881 average time/residue: 1.6236 time to fit residues: 1647.7250 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 : 3.318 ------------------------------------------------------------------------------- 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 152 LYS 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 474 LEU 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 73 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 318 PHE 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 B residue 573 PHE Chi-restraints excluded: chain B residue 651 THR 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 370 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 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 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 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 312 VAL Chi-restraints excluded: chain F residue 500 CYS Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE 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 362 ASN Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 395 SER 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 594 ILE Chi-restraints excluded: chain C residue 672 ASN 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 68 optimal weight: 0.6980 chunk 347 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 217 optimal weight: 0.4980 chunk 194 optimal weight: 0.9990 chunk 360 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 204 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** B 156 GLN B 305 ASN B 504 GLN D 156 GLN ** D 215 HIS ** 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 271 GLN C 276 ASN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 442 ASN C 481 GLN C 507 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.102992 restraints weight = 54905.976| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.86 r_work: 0.3407 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30865 Z= 0.137 Angle : 0.528 9.922 42028 Z= 0.272 Chirality : 0.047 0.266 4686 Planarity : 0.005 0.062 5563 Dihedral : 4.802 52.037 4166 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 2.90 % Allowed : 22.63 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3839 helix: 1.49 (0.21), residues: 620 sheet: 1.29 (0.15), residues: 1138 loop : 0.07 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 732 HIS 0.009 0.001 HIS A 215 PHE 0.018 0.001 PHE B 573 TYR 0.012 0.001 TYR D 725 ARG 0.013 0.000 ARG C 735 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 1112) hydrogen bonds : angle 5.25071 ( 3159) SS BOND : bond 0.00474 ( 5) SS BOND : angle 0.73467 ( 10) covalent geometry : bond 0.00320 (30860) covalent geometry : angle 0.52833 (42018) *********************** 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 933 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 836 time to evaluate : 3.420 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8592 (tttt) cc_final: 0.8388 (ttpt) REVERT: A 365 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8236 (ptp-170) REVERT: A 368 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7442 (mtt180) REVERT: A 428 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8470 (ptt-90) REVERT: B 99 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 167 PHE cc_start: 0.8443 (t80) cc_final: 0.8189 (t80) REVERT: B 318 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: D 151 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8459 (mmtm) REVERT: D 387 LEU cc_start: 0.8703 (mm) cc_final: 0.8496 (mp) REVERT: D 592 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8299 (p) REVERT: E 504 GLN cc_start: 0.8286 (tp-100) cc_final: 0.8066 (tp40) REVERT: F 224 ARG cc_start: 0.8656 (mtt90) cc_final: 0.8108 (mtt90) REVERT: F 309 ASN cc_start: 0.8136 (t0) cc_final: 0.7896 (t0) REVERT: C 436 GLN cc_start: 0.6553 (tt0) cc_final: 0.5684 (tt0) REVERT: C 524 TYR cc_start: 0.8331 (m-80) cc_final: 0.7791 (m-80) REVERT: C 527 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7234 (mt) REVERT: C 733 PHE cc_start: 0.8335 (p90) cc_final: 0.8099 (p90) outliers start: 97 outliers final: 66 residues processed: 881 average time/residue: 1.9921 time to fit residues: 2059.6703 Evaluate side-chains 902 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 830 time to evaluate : 3.399 ------------------------------------------------------------------------------- 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 152 LYS 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 474 LEU 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 73 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 318 PHE 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 573 PHE Chi-restraints excluded: chain B residue 651 THR 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 323 LYS Chi-restraints excluded: chain D residue 370 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 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 207 LEU 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 500 CYS Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 621 VAL 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 395 SER 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 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 136 optimal weight: 0.9980 chunk 246 optimal weight: 0.0670 chunk 141 optimal weight: 0.5980 chunk 322 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 374 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 117 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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** 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 179 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN F 327 GLN C 271 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 481 GLN C 504 GLN C 507 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104477 restraints weight = 64859.527| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.09 r_work: 0.3380 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 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 = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1708 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= 0.131 Angle : 0.527 8.892 42028 Z= 0.270 Chirality : 0.047 0.264 4686 Planarity : 0.005 0.085 5563 Dihedral : 4.793 52.343 4166 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 2.51 % Allowed : 23.28 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3839 helix: 1.51 (0.21), residues: 620 sheet: 1.28 (0.15), residues: 1137 loop : 0.07 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 732 HIS 0.009 0.001 HIS A 215 PHE 0.018 0.001 PHE B 573 TYR 0.020 0.001 TYR E 523 ARG 0.019 0.000 ARG C 169 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 1112) hydrogen bonds : angle 5.21578 ( 3159) SS BOND : bond 0.00435 ( 5) SS BOND : angle 0.70949 ( 10) covalent geometry : bond 0.00306 (30860) covalent geometry : angle 0.52689 (42018) *********************** 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 924 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 840 time to evaluate : 3.490 Fit side-chains revert: symmetry clash REVERT: A 350 LYS cc_start: 0.8638 (tttt) cc_final: 0.8432 (ttpt) REVERT: A 365 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8312 (ptp-170) REVERT: A 368 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7680 (mtt180) REVERT: A 428 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8491 (ptt-90) REVERT: A 612 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7606 (mtmm) REVERT: A 732 TRP cc_start: 0.7452 (p-90) cc_final: 0.7142 (p-90) REVERT: B 87 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8070 (ptm) REVERT: B 99 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7367 (mm-30) REVERT: B 167 PHE cc_start: 0.8503 (t80) cc_final: 0.8211 (t80) REVERT: B 318 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: D 151 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8468 (mmtm) REVERT: D 387 LEU cc_start: 0.8749 (mm) cc_final: 0.8531 (mp) REVERT: D 592 SER cc_start: 0.8611 (m) cc_final: 0.8310 (p) REVERT: F 224 ARG cc_start: 0.8691 (mtt90) cc_final: 0.8148 (mtt90) REVERT: F 309 ASN cc_start: 0.8188 (t0) cc_final: 0.7938 (t0) REVERT: C 263 GLN cc_start: 0.7820 (mp10) cc_final: 0.7592 (mp10) REVERT: C 436 GLN cc_start: 0.6758 (tt0) cc_final: 0.5875 (tt0) REVERT: C 524 TYR cc_start: 0.8386 (m-80) cc_final: 0.7855 (m-80) REVERT: C 527 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7206 (mt) REVERT: C 733 PHE cc_start: 0.8382 (p90) cc_final: 0.8175 (p90) outliers start: 84 outliers final: 66 residues processed: 879 average time/residue: 1.7428 time to fit residues: 1770.4721 Evaluate side-chains 908 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 836 time to evaluate : 3.566 ------------------------------------------------------------------------------- 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 152 LYS 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 474 LEU 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 73 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 318 PHE 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 470 SER Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 651 THR 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 297 LYS Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 573 PHE 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 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 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 500 CYS Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 621 VAL 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 395 SER 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 594 ILE 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 109 optimal weight: 0.9980 chunk 350 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 260 optimal weight: 0.3980 chunk 296 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 340 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 357 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** B 156 GLN B 305 ASN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 504 GLN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN C 271 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.117591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103521 restraints weight = 52403.112| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.83 r_work: 0.3377 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 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 = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30865 Z= 0.235 Angle : 0.587 13.600 42028 Z= 0.302 Chirality : 0.050 0.268 4686 Planarity : 0.005 0.064 5563 Dihedral : 5.037 51.768 4166 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 2.51 % Allowed : 23.52 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.13), residues: 3839 helix: 1.54 (0.22), residues: 590 sheet: 1.26 (0.15), residues: 1143 loop : 0.01 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 732 HIS 0.011 0.002 HIS A 215 PHE 0.021 0.002 PHE A 573 TYR 0.020 0.002 TYR A 403 ARG 0.014 0.001 ARG C 169 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1112) hydrogen bonds : angle 5.38482 ( 3159) SS BOND : bond 0.00659 ( 5) SS BOND : angle 1.00261 ( 10) covalent geometry : bond 0.00562 (30860) covalent geometry : angle 0.58694 (42018) ********************** 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 916 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 832 time to evaluate : 5.803 Fit side-chains revert: symmetry clash REVERT: A 365 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8236 (ptp-170) REVERT: A 368 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7629 (mtt180) REVERT: A 428 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8543 (ptt-90) REVERT: A 612 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7652 (mtmm) REVERT: B 99 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7380 (mm-30) REVERT: B 503 PHE cc_start: 0.8155 (p90) cc_final: 0.7902 (p90) REVERT: D 151 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8449 (mmtm) REVERT: D 365 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7456 (mtp180) REVERT: D 387 LEU cc_start: 0.8715 (mm) cc_final: 0.8504 (mp) REVERT: D 573 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8547 (p90) REVERT: D 592 SER cc_start: 0.8627 (m) cc_final: 0.8351 (p) REVERT: E 424 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8102 (mmtm) REVERT: F 224 ARG cc_start: 0.8685 (mtt90) cc_final: 0.8159 (mtt90) REVERT: F 309 ASN cc_start: 0.8198 (t0) cc_final: 0.7954 (t0) REVERT: C 263 GLN cc_start: 0.7884 (mp10) cc_final: 0.7680 (mp10) REVERT: C 412 MET cc_start: 0.7881 (ttp) cc_final: 0.7678 (ttp) REVERT: C 436 GLN cc_start: 0.6641 (tt0) cc_final: 0.5775 (tt0) REVERT: C 524 TYR cc_start: 0.8363 (m-80) cc_final: 0.7811 (m-80) REVERT: C 527 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7439 (mt) REVERT: C 733 PHE cc_start: 0.8390 (p90) cc_final: 0.8161 (p90) outliers start: 84 outliers final: 59 residues processed: 871 average time/residue: 2.0390 time to fit residues: 2093.2514 Evaluate side-chains 889 residues out of total 3349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 825 time to evaluate : 3.666 ------------------------------------------------------------------------------- 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 474 LEU 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 73 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 241 VAL 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 651 THR 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 323 LYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 622 GLN 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 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 157 MET Chi-restraints excluded: chain F residue 207 LEU 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 500 CYS Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 481 GLN 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 721 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 159 optimal weight: 0.0980 chunk 377 optimal weight: 0.5980 chunk 206 optimal weight: 0.9980 chunk 247 optimal weight: 0.0470 chunk 335 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 179 optimal weight: 0.0870 chunk 160 optimal weight: 0.0570 overall best weight: 0.1774 ------------------------------------------------------------------------------- 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** B 95 ASN B 305 ASN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN C 271 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 504 GLN C 507 GLN C 569 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.118030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103952 restraints weight = 55726.535| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.89 r_work: 0.3413 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30865 Z= 0.102 Angle : 0.532 8.916 42028 Z= 0.273 Chirality : 0.046 0.256 4686 Planarity : 0.005 0.060 5563 Dihedral : 4.805 52.420 4166 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.76 % Allowed : 24.33 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3839 helix: 1.51 (0.21), residues: 626 sheet: 1.22 (0.15), residues: 1128 loop : 0.06 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 260 HIS 0.011 0.001 HIS B 215 PHE 0.022 0.001 PHE B 573 TYR 0.018 0.001 TYR E 523 ARG 0.013 0.000 ARG C 735 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 1112) hydrogen bonds : angle 5.21035 ( 3159) SS BOND : bond 0.00310 ( 5) SS BOND : angle 0.50817 ( 10) covalent geometry : bond 0.00229 (30860) covalent geometry : angle 0.53230 (42018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44096.25 seconds wall clock time: 775 minutes 17.00 seconds (46517.00 seconds total)