Starting phenix.real_space_refine on Mon Sep 14 21:01:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r7s_24302/09_2026/7r7s_24302.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7s_24302/09_2026/7r7s_24302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7r7s_24302/09_2026/7r7s_24302.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r7s_24302/09_2026/7r7s_24302.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r7s_24302/09_2026/7r7s_24302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7s_24302/09_2026/7r7s_24302.map" model { file = "/net/cci-nas-00/data/ceres_data/7r7s_24302/09_2026/7r7s_24302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7s_24302/09_2026/7r7s_24302.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 180 5.16 5 C 20791 2.51 5 N 5916 2.21 5 O 6316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33239 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5680 Classifications: {'peptide': 722} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 681} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 521} Chain breaks: 4 Chain: "C" Number of atoms: 4272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4272 Classifications: {'peptide': 546} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 516} Chain breaks: 2 Chain: "D" Number of atoms: 5662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5662 Classifications: {'peptide': 721} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 680} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 5632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5632 Classifications: {'peptide': 717} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 677} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 5757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5757 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 692} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 802 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "J" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 758 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.17, per 1000 atoms: 0.22 Number of scatterers: 33239 At special positions: 0 Unit cell: (128.583, 168.147, 176.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 36 15.00 O 6316 8.00 N 5916 7.00 C 20791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7894 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 31 sheets defined 43.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.665A pdb=" N GLY A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.657A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.738A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.820A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix removed outlier: 3.678A pdb=" N HIS A 499 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.508A pdb=" N LYS A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.751A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 578 through 583 removed outlier: 4.088A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 583' Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 598 through 610 removed outlier: 4.261A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.905A pdb=" N ILE A 628 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 625 through 629' Processing helix chain 'A' and resid 649 through 659 removed outlier: 4.426A pdb=" N ARG A 653 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 654 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 655 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 656 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 657 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 659 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.903A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 713 Processing helix chain 'A' and resid 732 through 742 removed outlier: 4.341A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.549A pdb=" N LEU B 213 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.857A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.611A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.668A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.694A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 removed outlier: 4.284A pdb=" N ILE B 479 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 removed outlier: 3.611A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.772A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.050A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 3.750A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 610 removed outlier: 4.197A pdb=" N ILE B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 removed outlier: 3.558A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 678 Processing helix chain 'B' and resid 686 through 712 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.835A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 758 Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.615A pdb=" N ASP C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 206' Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.681A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'C' and resid 285 through 296 removed outlier: 3.904A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.938A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 4.005A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.666A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 removed outlier: 3.704A pdb=" N LYS C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.735A pdb=" N HIS C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 removed outlier: 4.137A pdb=" N LYS C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 552 removed outlier: 3.897A pdb=" N LEU C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.810A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 588 Processing helix chain 'C' and resid 599 through 609 removed outlier: 3.726A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.815A pdb=" N ILE C 628 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 625 through 629' Processing helix chain 'C' and resid 651 through 660 removed outlier: 3.822A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 678 Processing helix chain 'C' and resid 688 through 713 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.828A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 758 Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.535A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 removed outlier: 3.861A pdb=" N VAL D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.530A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.550A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 250 through 263 removed outlier: 3.521A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 282 through 293 removed outlier: 4.095A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS D 288 " --> pdb=" O SER D 284 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.901A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 335 removed outlier: 3.620A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.509A pdb=" N THR D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.811A pdb=" N ILE D 479 " --> pdb=" O TRP D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.549A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 504 Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 544 through 553 removed outlier: 3.568A pdb=" N GLY D 553 " --> pdb=" O THR D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.278A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 removed outlier: 3.887A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.545A pdb=" N LEU D 634 " --> pdb=" O PRO D 631 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 659 Processing helix chain 'D' and resid 671 through 678 removed outlier: 3.964A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 713 removed outlier: 3.869A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.787A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 758 Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.660A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 285 through 296 removed outlier: 3.914A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.545A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.722A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 4.045A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 407 through 426 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 483 through 498 removed outlier: 4.215A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.781A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 553 removed outlier: 3.620A pdb=" N LEU E 548 " --> pdb=" O GLY E 544 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY E 553 " --> pdb=" O THR E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 569 removed outlier: 4.227A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 585 removed outlier: 4.086A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 3.658A pdb=" N ASP E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 659 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.666A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 713 removed outlier: 3.671A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 4.017A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 758 Processing helix chain 'E' and resid 759 through 761 No H-bonds generated for 'chain 'E' and resid 759 through 761' Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.886A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.757A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 425 removed outlier: 3.789A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 445 removed outlier: 3.879A pdb=" N LEU F 445 " --> pdb=" O MET F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.589A pdb=" N ILE F 479 " --> pdb=" O TRP F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.686A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.935A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 544 through 553 removed outlier: 4.092A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.770A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 585 removed outlier: 3.604A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 611 removed outlier: 3.750A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 656 removed outlier: 4.301A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 679 removed outlier: 4.148A pdb=" N ALA F 676 " --> pdb=" O LEU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 713 Processing helix chain 'F' and resid 732 through 742 removed outlier: 4.015A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 758 Processing helix chain 'I' and resid 272 through 286 removed outlier: 4.070A pdb=" N ALA I 277 " --> pdb=" O PRO I 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU I 278 " --> pdb=" O ALA I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 329 Processing helix chain 'I' and resid 330 through 334 removed outlier: 3.613A pdb=" N ALA I 333 " --> pdb=" O PRO I 330 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA I 334 " --> pdb=" O ALA I 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 330 through 334' Processing helix chain 'J' and resid 272 through 287 removed outlier: 4.163A pdb=" N ALA J 277 " --> pdb=" O PRO J 273 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU J 278 " --> pdb=" O ALA J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 329 Processing helix chain 'J' and resid 330 through 335 removed outlier: 4.249A pdb=" N ALA J 334 " --> pdb=" O PRO J 330 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 330 through 335' Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.662A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 176 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 146 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 266 removed outlier: 5.625A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 342 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 266 removed outlier: 5.522A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 266 removed outlier: 5.522A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 301 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 346 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 543 removed outlier: 7.027A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 265 through 266 removed outlier: 5.727A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 342 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 538 through 540 removed outlier: 7.041A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 29 removed outlier: 6.975A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 151 through 155 removed outlier: 5.621A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.664A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 344 through 346 removed outlier: 6.892A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 269 through 270 removed outlier: 7.223A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.154A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 622 " --> pdb=" O PHE D 576 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 29 removed outlier: 7.159A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 151 through 155 removed outlier: 3.771A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC2, first strand: chain 'E' and resid 269 through 270 removed outlier: 7.514A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 346 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 265 through 266 removed outlier: 6.020A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 541 through 543 removed outlier: 3.606A pdb=" N ILE E 542 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP E 577 " --> pdb=" O ILE E 542 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 82 through 84 removed outlier: 5.954A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 38 through 40 removed outlier: 3.782A pdb=" N LEU F 58 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 116 through 118 Processing sheet with id=AC8, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=AC9, first strand: chain 'F' and resid 269 through 270 removed outlier: 3.888A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 620 through 623 removed outlier: 6.441A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 538 through 543 Processing sheet with id=AD3, first strand: chain 'I' and resid 300 through 301 removed outlier: 3.596A pdb=" N ARG I 368 " --> pdb=" O VAL I 338 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU I 339 " --> pdb=" O LEU I 348 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 299 through 301 removed outlier: 3.510A pdb=" N ARG J 368 " --> pdb=" O VAL J 338 " (cutoff:3.500A) 1175 hydrogen bonds defined for protein. 3405 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: 7.02 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11468 1.37 - 1.51: 8508 1.51 - 1.66: 13527 1.66 - 1.80: 196 1.80 - 1.95: 90 Bond restraints: 33789 Sorted by residual: bond pdb=" C LEU B 222 " pdb=" N PRO B 223 " ideal model delta sigma weight residual 1.335 1.391 -0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" C SER E 171 " pdb=" N PRO E 172 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.25e+00 bond pdb=" C ARG C 635 " pdb=" N PRO C 636 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.83e+00 bond pdb=" N PRO F 237 " pdb=" CA PRO F 237 " ideal model delta sigma weight residual 1.465 1.508 -0.043 2.03e-02 2.43e+03 4.44e+00 bond pdb=" CA THR A 475 " pdb=" CB THR A 475 " ideal model delta sigma weight residual 1.530 1.566 -0.036 1.69e-02 3.50e+03 4.43e+00 ... (remaining 33784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 45052 3.29 - 6.59: 517 6.59 - 9.88: 113 9.88 - 13.17: 13 13.17 - 16.47: 3 Bond angle restraints: 45698 Sorted by residual: angle pdb=" C ASN A 199 " pdb=" N GLU A 200 " pdb=" CA GLU A 200 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" CA LYS F 236 " pdb=" CB LYS F 236 " pdb=" CG LYS F 236 " ideal model delta sigma weight residual 114.10 125.70 -11.60 2.00e+00 2.50e-01 3.37e+01 angle pdb=" C LEU F 464 " pdb=" N ARG F 465 " pdb=" CA ARG F 465 " ideal model delta sigma weight residual 121.54 132.06 -10.52 1.91e+00 2.74e-01 3.04e+01 angle pdb=" CA ARG D 22 " pdb=" CB ARG D 22 " pdb=" CG ARG D 22 " ideal model delta sigma weight residual 114.10 125.05 -10.95 2.00e+00 2.50e-01 3.00e+01 angle pdb=" C SER E 284 " pdb=" N ASN E 285 " pdb=" CA ASN E 285 " ideal model delta sigma weight residual 121.54 131.90 -10.36 1.91e+00 2.74e-01 2.94e+01 ... (remaining 45693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.92: 19769 27.92 - 55.84: 1015 55.84 - 83.75: 83 83.75 - 111.67: 7 111.67 - 139.59: 4 Dihedral angle restraints: 20878 sinusoidal: 8746 harmonic: 12132 Sorted by residual: dihedral pdb=" CA PHE I 343 " pdb=" C PHE I 343 " pdb=" N PRO I 344 " pdb=" CA PRO I 344 " ideal model delta harmonic sigma weight residual 180.00 131.54 48.46 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA PRO D 237 " pdb=" C PRO D 237 " pdb=" N PRO D 238 " pdb=" CA PRO D 238 " ideal model delta harmonic sigma weight residual -180.00 -131.56 -48.44 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA PRO A 237 " pdb=" C PRO A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta harmonic sigma weight residual -180.00 -132.01 -47.99 0 5.00e+00 4.00e-02 9.21e+01 ... (remaining 20875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4811 0.106 - 0.213: 320 0.213 - 0.319: 31 0.319 - 0.425: 3 0.425 - 0.532: 2 Chirality restraints: 5167 Sorted by residual: chirality pdb=" CB ILE D 233 " pdb=" CA ILE D 233 " pdb=" CG1 ILE D 233 " pdb=" CG2 ILE D 233 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CB ILE E 233 " pdb=" CA ILE E 233 " pdb=" CG1 ILE E 233 " pdb=" CG2 ILE E 233 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 5164 not shown) Planarity restraints: 5980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 506 " -0.034 2.00e-02 2.50e+03 3.02e-02 1.60e+01 pdb=" CG PHE B 506 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 506 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 506 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 506 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 506 " -0.017 2.00e-02 2.50e+03 pdb=" CZ PHE B 506 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 222 " 0.057 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO C 223 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 343 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO I 344 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO I 344 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO I 344 " -0.047 5.00e-02 4.00e+02 ... (remaining 5977 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9435 2.81 - 3.34: 30413 3.34 - 3.86: 54741 3.86 - 4.38: 60795 4.38 - 4.90: 100716 Nonbonded interactions: 256100 Sorted by model distance: nonbonded pdb=" O VAL E 258 " pdb=" OG1 THR E 262 " model vdw 2.294 3.040 nonbonded pdb=" O LEU B 381 " pdb=" OG1 THR B 385 " model vdw 2.306 3.040 nonbonded pdb=" O PRO C 272 " pdb=" OG SER C 276 " model vdw 2.308 3.040 nonbonded pdb=" O2G AGS F 902 " pdb=" O3A AGS F 902 " model vdw 2.321 3.040 nonbonded pdb=" O CYS F 522 " pdb=" O2B AGS F 902 " model vdw 2.322 3.040 ... (remaining 256095 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 22 through 660 or resid 666 through 767 or resid 901 throu \ gh 902)) selection = (chain 'D' and (resid 22 through 553 or resid 557 through 587 or resid 596 throu \ gh 660 or resid 666 through 902)) selection = (chain 'E' and (resid 22 through 431 or resid 439 through 553 or resid 557 throu \ gh 587 or resid 596 through 902)) selection = (chain 'F' and (resid 22 through 553 or resid 557 through 587 or resid 596 throu \ gh 660 or resid 666 through 767 or resid 901 through 902)) } ncs_group { reference = (chain 'B' and (resid 199 through 431 or resid 439 through 588 or resid 597 thro \ ugh 713 or resid 726 through 768 or resid 901 through 902)) selection = (chain 'C' and (resid 199 through 588 or resid 597 through 902)) } ncs_group { reference = (chain 'I' and resid 267 through 370) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.480 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 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 : 0.004 0.060 33789 Z= 0.212 Angle : 0.961 16.466 45698 Z= 0.519 Chirality : 0.058 0.532 5167 Planarity : 0.007 0.086 5980 Dihedral : 15.641 139.588 12984 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.26 % Favored : 90.64 % Rotamer: Outliers : 0.03 % Allowed : 0.82 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 4.87 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.11), residues: 4157 helix: -1.77 (0.10), residues: 1626 sheet: -1.33 (0.23), residues: 496 loop : -2.56 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 453 TYR 0.020 0.002 TYR F 173 PHE 0.068 0.002 PHE B 506 TRP 0.020 0.002 TRP A 476 HIS 0.005 0.001 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (33789) covalent geometry : angle 0.96063 / 0.52 (45698) hydrogen bonds : bond 0.17276 / 11.48 ( 1175) hydrogen bonds : angle 7.07099 / 4.90 ( 3405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 904 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.7757 (tp) cc_final: 0.7505 (tp) REVERT: A 296 ASN cc_start: 0.5073 (t0) cc_final: 0.4111 (t0) REVERT: A 379 GLU cc_start: 0.8444 (tt0) cc_final: 0.7661 (tp30) REVERT: A 561 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8627 (tm-30) REVERT: A 564 ASP cc_start: 0.8958 (t0) cc_final: 0.8693 (t0) REVERT: A 577 ASP cc_start: 0.8232 (t0) cc_final: 0.6494 (t70) REVERT: A 607 GLU cc_start: 0.8154 (mm-30) cc_final: 0.6974 (mt-10) REVERT: A 620 ILE cc_start: 0.9214 (mt) cc_final: 0.8954 (pt) REVERT: A 765 SER cc_start: 0.8522 (m) cc_final: 0.8144 (t) REVERT: B 244 TYR cc_start: 0.7660 (p90) cc_final: 0.7297 (p90) REVERT: B 274 ILE cc_start: 0.8283 (tp) cc_final: 0.7764 (tp) REVERT: B 388 MET cc_start: 0.7683 (ppp) cc_final: 0.7042 (ppp) REVERT: B 414 LEU cc_start: 0.8495 (tp) cc_final: 0.8196 (tp) REVERT: B 546 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8233 (tp30) REVERT: B 561 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8141 (tp30) REVERT: B 562 ILE cc_start: 0.9593 (mm) cc_final: 0.9378 (mm) REVERT: B 602 ASN cc_start: 0.8966 (m-40) cc_final: 0.8755 (m-40) REVERT: B 604 ILE cc_start: 0.9369 (mm) cc_final: 0.9144 (mm) REVERT: B 609 ASP cc_start: 0.7918 (t0) cc_final: 0.7264 (t0) REVERT: B 736 PHE cc_start: 0.8212 (m-80) cc_final: 0.7980 (m-80) REVERT: C 274 ILE cc_start: 0.8899 (mm) cc_final: 0.8526 (mm) REVERT: C 302 PHE cc_start: 0.6898 (t80) cc_final: 0.6623 (t80) REVERT: C 315 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7176 (tptt) REVERT: C 364 ASP cc_start: 0.7748 (p0) cc_final: 0.7528 (p0) REVERT: C 562 ILE cc_start: 0.9228 (mm) cc_final: 0.8790 (mm) REVERT: C 564 ASP cc_start: 0.8667 (t0) cc_final: 0.8201 (t0) REVERT: C 603 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8872 (tp-100) REVERT: D 84 MET cc_start: 0.5185 (ptp) cc_final: 0.4912 (ptt) REVERT: D 132 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6827 (mp0) REVERT: D 148 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8197 (ttmm) REVERT: D 239 ARG cc_start: 0.6914 (ttt180) cc_final: 0.6533 (mmt180) REVERT: D 529 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8570 (pttm) REVERT: D 551 TRP cc_start: 0.6190 (t60) cc_final: 0.5812 (t60) REVERT: D 602 ASN cc_start: 0.9120 (t0) cc_final: 0.8568 (t0) REVERT: D 653 ARG cc_start: 0.6708 (pmt170) cc_final: 0.6466 (ppt170) REVERT: E 46 MET cc_start: 0.4833 (mtp) cc_final: 0.4629 (mtt) REVERT: E 219 MET cc_start: 0.7630 (mmt) cc_final: 0.7172 (mmm) REVERT: E 332 MET cc_start: 0.6603 (ttt) cc_final: 0.6040 (ttt) REVERT: E 466 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6243 (tm-30) REVERT: E 602 ASN cc_start: 0.9235 (m-40) cc_final: 0.8773 (t0) REVERT: E 628 ILE cc_start: 0.7896 (pt) cc_final: 0.7578 (mt) REVERT: E 690 ILE cc_start: 0.8140 (mm) cc_final: 0.7912 (mp) REVERT: F 194 GLU cc_start: 0.7810 (tt0) cc_final: 0.7277 (mp0) REVERT: F 269 ILE cc_start: 0.8659 (mm) cc_final: 0.8442 (mt) REVERT: F 351 ASN cc_start: 0.8420 (p0) cc_final: 0.6475 (p0) REVERT: F 411 LEU cc_start: 0.8458 (tp) cc_final: 0.8001 (tp) REVERT: F 560 ARG cc_start: 0.8486 (mtt180) cc_final: 0.7902 (mtt-85) REVERT: F 607 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7962 (mm-30) REVERT: I 332 MET cc_start: 0.2924 (mmp) cc_final: 0.2581 (mmm) REVERT: J 341 THR cc_start: 0.5620 (p) cc_final: 0.4949 (p) REVERT: J 365 ILE cc_start: 0.5972 (mt) cc_final: 0.5624 (mt) outliers start: 1 outliers final: 0 residues processed: 905 average time/residue: 0.2459 time to fit residues: 345.9294 Evaluate side-chains 515 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 40.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN B 285 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 327 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 285 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 36 ASN E 296 ASN E 494 GLN F 85 ASN ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.104118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.079401 restraints weight = 123108.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.081108 restraints weight = 83006.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.082302 restraints weight = 62617.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.083127 restraints weight = 50952.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.083759 restraints weight = 44092.328| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33789 Z= 0.175 Angle : 0.718 13.564 45698 Z= 0.373 Chirality : 0.047 0.289 5167 Planarity : 0.006 0.124 5980 Dihedral : 8.424 129.087 4666 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.06 % Favored : 91.89 % Rotamer: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 3.10 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.12), residues: 4157 helix: -0.48 (0.12), residues: 1644 sheet: -1.20 (0.23), residues: 502 loop : -2.38 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 653 TYR 0.013 0.001 TYR F 173 PHE 0.034 0.002 PHE B 506 TRP 0.023 0.002 TRP C 454 HIS 0.005 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (33789) covalent geometry : angle 0.71773 / 0.37 (45698) hydrogen bonds : bond 0.03980 / 2.69 ( 1175) hydrogen bonds : angle 5.66566 / 3.96 ( 3405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 619 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8294 (tt0) REVERT: A 274 ILE cc_start: 0.9005 (tp) cc_final: 0.8760 (tp) REVERT: A 296 ASN cc_start: 0.6694 (t0) cc_final: 0.5072 (t0) REVERT: A 312 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8805 (ttpp) REVERT: A 330 THR cc_start: 0.8235 (m) cc_final: 0.7877 (p) REVERT: A 379 GLU cc_start: 0.9385 (tt0) cc_final: 0.8784 (tp30) REVERT: A 561 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8909 (tm-30) REVERT: A 575 PHE cc_start: 0.8688 (t80) cc_final: 0.8392 (t80) REVERT: A 577 ASP cc_start: 0.8038 (t0) cc_final: 0.6064 (t70) REVERT: A 578 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 642 LEU cc_start: 0.9124 (mp) cc_final: 0.8653 (pt) REVERT: A 673 GLU cc_start: 0.9072 (pm20) cc_final: 0.8597 (pp20) REVERT: A 765 SER cc_start: 0.9212 (m) cc_final: 0.8822 (t) REVERT: B 244 TYR cc_start: 0.8819 (p90) cc_final: 0.8239 (p90) REVERT: B 274 ILE cc_start: 0.9188 (tp) cc_final: 0.8980 (tp) REVERT: B 305 GLU cc_start: 0.9272 (tp30) cc_final: 0.9064 (tp30) REVERT: B 388 MET cc_start: 0.8154 (ppp) cc_final: 0.7331 (ppp) REVERT: B 562 ILE cc_start: 0.9507 (mm) cc_final: 0.9212 (mm) REVERT: B 572 CYS cc_start: 0.5528 (p) cc_final: 0.5216 (p) REVERT: B 602 ASN cc_start: 0.8980 (m-40) cc_final: 0.8740 (m-40) REVERT: B 736 PHE cc_start: 0.9119 (m-80) cc_final: 0.8789 (m-80) REVERT: C 348 ASN cc_start: 0.8785 (p0) cc_final: 0.8366 (t0) REVERT: C 402 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7063 (mt-10) REVERT: C 486 LYS cc_start: 0.7197 (tttt) cc_final: 0.6776 (tttp) REVERT: C 564 ASP cc_start: 0.9131 (t0) cc_final: 0.8788 (t0) REVERT: C 602 ASN cc_start: 0.8666 (m110) cc_final: 0.8301 (t0) REVERT: C 603 GLN cc_start: 0.9604 (tp-100) cc_final: 0.9320 (tp-100) REVERT: D 84 MET cc_start: 0.5927 (ptp) cc_final: 0.5525 (ptt) REVERT: D 132 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6687 (mp0) REVERT: D 148 LYS cc_start: 0.8231 (tmtt) cc_final: 0.7987 (ttmm) REVERT: D 291 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8660 (tp30) REVERT: D 314 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8769 (tm-30) REVERT: D 326 SER cc_start: 0.8976 (m) cc_final: 0.8745 (p) REVERT: D 332 MET cc_start: 0.7755 (tpt) cc_final: 0.7370 (tpp) REVERT: D 411 LEU cc_start: 0.9219 (mp) cc_final: 0.8918 (mp) REVERT: D 538 ASN cc_start: 0.7902 (t0) cc_final: 0.7587 (t0) REVERT: D 550 MET cc_start: 0.7332 (ptp) cc_final: 0.6974 (ptp) REVERT: D 602 ASN cc_start: 0.8992 (t0) cc_final: 0.8493 (t0) REVERT: D 653 ARG cc_start: 0.8507 (pmt170) cc_final: 0.8137 (ppt170) REVERT: D 757 MET cc_start: 0.7912 (ptt) cc_final: 0.7564 (ptp) REVERT: E 83 ARG cc_start: 0.5705 (mtp180) cc_final: 0.5462 (mtm180) REVERT: E 158 MET cc_start: 0.6507 (tmm) cc_final: 0.5372 (ptt) REVERT: E 244 TYR cc_start: 0.8995 (p90) cc_final: 0.8062 (p90) REVERT: E 291 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: E 332 MET cc_start: 0.8809 (ttt) cc_final: 0.8322 (ttt) REVERT: E 427 MET cc_start: 0.8409 (ppp) cc_final: 0.7629 (ppp) REVERT: E 449 MET cc_start: 0.8133 (pmm) cc_final: 0.7847 (pmm) REVERT: E 508 MET cc_start: 0.5812 (ttm) cc_final: 0.5231 (ttm) REVERT: E 564 ASP cc_start: 0.9061 (t0) cc_final: 0.8806 (t0) REVERT: E 567 ARG cc_start: 0.9010 (mtp180) cc_final: 0.8584 (mtm-85) REVERT: E 674 PHE cc_start: 0.8221 (t80) cc_final: 0.8019 (t80) REVERT: E 695 CYS cc_start: 0.8817 (m) cc_final: 0.7964 (m) REVERT: F 194 GLU cc_start: 0.8595 (tt0) cc_final: 0.7754 (mp0) REVERT: F 205 ASP cc_start: 0.8405 (t0) cc_final: 0.8116 (t0) REVERT: F 344 MET cc_start: 0.8681 (ptp) cc_final: 0.8263 (pmm) REVERT: F 354 ASP cc_start: 0.8767 (t70) cc_final: 0.8559 (t0) REVERT: F 508 MET cc_start: 0.7379 (mmm) cc_final: 0.7161 (tpp) REVERT: F 560 ARG cc_start: 0.8870 (mtt180) cc_final: 0.8594 (mtt-85) REVERT: F 577 ASP cc_start: 0.8307 (t0) cc_final: 0.8008 (t0) REVERT: F 578 GLU cc_start: 0.8398 (pt0) cc_final: 0.7811 (pt0) REVERT: F 580 ASP cc_start: 0.7978 (m-30) cc_final: 0.7673 (m-30) REVERT: F 607 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8794 (mm-30) REVERT: F 615 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8104 (mtmm) REVERT: I 332 MET cc_start: 0.3508 (mmp) cc_final: 0.3209 (mmm) outliers start: 3 outliers final: 1 residues processed: 622 average time/residue: 0.2263 time to fit residues: 223.2182 Evaluate side-chains 449 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 413 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 291 optimal weight: 9.9990 chunk 183 optimal weight: 0.0980 chunk 137 optimal weight: 5.9990 chunk 407 optimal weight: 30.0000 chunk 284 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 376 optimal weight: 0.9980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 299 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.102760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.078095 restraints weight = 124340.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.079918 restraints weight = 83089.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.080865 restraints weight = 62841.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.081850 restraints weight = 52062.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.082334 restraints weight = 44462.409| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33789 Z= 0.178 Angle : 0.693 10.605 45698 Z= 0.360 Chirality : 0.046 0.239 5167 Planarity : 0.006 0.161 5980 Dihedral : 8.278 126.920 4666 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.64 % Favored : 91.34 % Rotamer: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 4157 helix: -0.09 (0.13), residues: 1642 sheet: -1.33 (0.23), residues: 518 loop : -2.26 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 638 TYR 0.023 0.002 TYR F 143 PHE 0.029 0.002 PHE E 265 TRP 0.028 0.003 TRP B 551 HIS 0.006 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (33789) covalent geometry : angle 0.69347 / 0.36 (45698) hydrogen bonds : bond 0.03751 / 2.53 ( 1175) hydrogen bonds : angle 5.47507 / 3.82 ( 3405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 574 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8732 (ttpp) REVERT: A 330 THR cc_start: 0.8315 (m) cc_final: 0.8066 (p) REVERT: A 379 GLU cc_start: 0.9421 (tt0) cc_final: 0.8800 (tp30) REVERT: A 397 GLU cc_start: 0.8675 (mp0) cc_final: 0.8025 (mp0) REVERT: A 442 MET cc_start: 0.6787 (mmt) cc_final: 0.6546 (mmt) REVERT: A 561 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8822 (tm-30) REVERT: A 575 PHE cc_start: 0.8647 (t80) cc_final: 0.7476 (t80) REVERT: A 577 ASP cc_start: 0.8089 (t0) cc_final: 0.7066 (t70) REVERT: A 630 ASP cc_start: 0.8860 (m-30) cc_final: 0.8605 (m-30) REVERT: A 634 LEU cc_start: 0.8700 (tt) cc_final: 0.8472 (tt) REVERT: A 642 LEU cc_start: 0.9064 (mp) cc_final: 0.8644 (pt) REVERT: A 674 PHE cc_start: 0.8568 (m-80) cc_final: 0.8324 (t80) REVERT: A 704 GLU cc_start: 0.9031 (tp30) cc_final: 0.8808 (tm-30) REVERT: A 765 SER cc_start: 0.9233 (m) cc_final: 0.8641 (t) REVERT: B 203 TYR cc_start: 0.7214 (t80) cc_final: 0.6897 (t80) REVERT: B 242 LEU cc_start: 0.9102 (mp) cc_final: 0.8900 (mp) REVERT: B 244 TYR cc_start: 0.8812 (p90) cc_final: 0.8245 (p90) REVERT: B 316 THR cc_start: 0.8436 (p) cc_final: 0.8216 (p) REVERT: B 388 MET cc_start: 0.8130 (ppp) cc_final: 0.7385 (ppp) REVERT: B 562 ILE cc_start: 0.9433 (mm) cc_final: 0.9071 (mm) REVERT: B 572 CYS cc_start: 0.5599 (p) cc_final: 0.5377 (p) REVERT: B 602 ASN cc_start: 0.8979 (m-40) cc_final: 0.8697 (m-40) REVERT: B 736 PHE cc_start: 0.9080 (m-80) cc_final: 0.8799 (m-80) REVERT: C 384 HIS cc_start: 0.7570 (m90) cc_final: 0.7178 (m90) REVERT: C 388 MET cc_start: 0.8150 (ptp) cc_final: 0.6204 (ppp) REVERT: C 402 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7209 (mt-10) REVERT: C 560 ARG cc_start: 0.9339 (ttp80) cc_final: 0.8988 (tpp80) REVERT: C 561 GLU cc_start: 0.8615 (pp20) cc_final: 0.8352 (pp20) REVERT: C 564 ASP cc_start: 0.9082 (t0) cc_final: 0.8750 (t0) REVERT: C 602 ASN cc_start: 0.8696 (m110) cc_final: 0.8269 (t0) REVERT: C 603 GLN cc_start: 0.9634 (tp-100) cc_final: 0.9195 (tp-100) REVERT: C 607 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8404 (tp30) REVERT: C 620 ILE cc_start: 0.9263 (mt) cc_final: 0.8830 (pt) REVERT: D 84 MET cc_start: 0.5961 (ptp) cc_final: 0.5573 (ptt) REVERT: D 132 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6711 (mp0) REVERT: D 291 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8562 (tp30) REVERT: D 314 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8716 (tm-30) REVERT: D 326 SER cc_start: 0.9084 (m) cc_final: 0.8811 (p) REVERT: D 332 MET cc_start: 0.7932 (tpt) cc_final: 0.7498 (tpp) REVERT: D 411 LEU cc_start: 0.9331 (mp) cc_final: 0.9092 (mp) REVERT: D 449 MET cc_start: 0.7937 (ptt) cc_final: 0.7081 (tmm) REVERT: D 515 LEU cc_start: 0.9316 (tt) cc_final: 0.9109 (mt) REVERT: D 538 ASN cc_start: 0.8004 (t0) cc_final: 0.7623 (t0) REVERT: D 602 ASN cc_start: 0.9049 (t0) cc_final: 0.8546 (t0) REVERT: D 653 ARG cc_start: 0.8565 (pmt170) cc_final: 0.8039 (ppt170) REVERT: D 757 MET cc_start: 0.7945 (ptt) cc_final: 0.7663 (ptp) REVERT: E 45 LYS cc_start: 0.8840 (tmmt) cc_final: 0.8603 (pttt) REVERT: E 110 TYR cc_start: 0.6543 (m-10) cc_final: 0.6167 (t80) REVERT: E 158 MET cc_start: 0.4810 (tmm) cc_final: 0.4364 (ptt) REVERT: E 427 MET cc_start: 0.8374 (ppp) cc_final: 0.7663 (ppp) REVERT: E 449 MET cc_start: 0.8077 (pmm) cc_final: 0.7847 (pmm) REVERT: E 508 MET cc_start: 0.5925 (ttm) cc_final: 0.5665 (ttm) REVERT: E 549 THR cc_start: 0.7940 (p) cc_final: 0.7567 (p) REVERT: E 564 ASP cc_start: 0.9041 (t0) cc_final: 0.8711 (t0) REVERT: E 567 ARG cc_start: 0.8967 (mtp180) cc_final: 0.8542 (mtm-85) REVERT: E 690 ILE cc_start: 0.8502 (mp) cc_final: 0.8235 (mp) REVERT: F 173 TYR cc_start: 0.7277 (p90) cc_final: 0.6832 (p90) REVERT: F 194 GLU cc_start: 0.8521 (tt0) cc_final: 0.7679 (mp0) REVERT: F 205 ASP cc_start: 0.8532 (t0) cc_final: 0.8172 (t0) REVERT: F 315 LYS cc_start: 0.9563 (tptp) cc_final: 0.9343 (tptt) REVERT: F 354 ASP cc_start: 0.8633 (t70) cc_final: 0.8402 (t0) REVERT: F 397 GLU cc_start: 0.9315 (mp0) cc_final: 0.9005 (mp0) REVERT: F 508 MET cc_start: 0.7636 (mmm) cc_final: 0.7319 (mmm) REVERT: F 560 ARG cc_start: 0.8764 (mtt180) cc_final: 0.8427 (mtt-85) REVERT: F 564 ASP cc_start: 0.9438 (m-30) cc_final: 0.9196 (m-30) REVERT: F 577 ASP cc_start: 0.8453 (t0) cc_final: 0.8080 (t0) REVERT: F 580 ASP cc_start: 0.8174 (m-30) cc_final: 0.7903 (m-30) REVERT: F 606 THR cc_start: 0.8644 (m) cc_final: 0.8344 (p) REVERT: F 607 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8777 (mm-30) REVERT: F 630 ASP cc_start: 0.8713 (t0) cc_final: 0.8435 (t0) REVERT: I 332 MET cc_start: 0.3476 (mmp) cc_final: 0.3156 (mmm) outliers start: 4 outliers final: 1 residues processed: 577 average time/residue: 0.2254 time to fit residues: 208.4041 Evaluate side-chains 438 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 437 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 53 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 300 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 403 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 660 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN F 602 ASN ** J 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.104630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.078950 restraints weight = 128421.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.080922 restraints weight = 84267.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.082091 restraints weight = 62437.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.083151 restraints weight = 50608.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.083736 restraints weight = 42597.488| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33789 Z= 0.127 Angle : 0.664 12.996 45698 Z= 0.339 Chirality : 0.046 0.240 5167 Planarity : 0.005 0.083 5980 Dihedral : 8.120 124.678 4666 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.77 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.13), residues: 4157 helix: 0.06 (0.13), residues: 1646 sheet: -1.29 (0.22), residues: 526 loop : -2.25 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 625 TYR 0.029 0.001 TYR A 495 PHE 0.026 0.002 PHE A 552 TRP 0.021 0.002 TRP A 454 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (33789) covalent geometry : angle 0.66431 / 0.34 (45698) hydrogen bonds : bond 0.03343 / 2.25 ( 1175) hydrogen bonds : angle 5.24349 / 3.65 ( 3405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.7888 (pm20) cc_final: 0.7490 (pm20) REVERT: A 312 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8674 (ttpp) REVERT: A 330 THR cc_start: 0.8117 (m) cc_final: 0.7828 (p) REVERT: A 379 GLU cc_start: 0.9409 (tt0) cc_final: 0.8806 (tp30) REVERT: A 395 ASP cc_start: 0.8506 (p0) cc_final: 0.8163 (p0) REVERT: A 561 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8829 (tm-30) REVERT: A 575 PHE cc_start: 0.8508 (t80) cc_final: 0.7809 (t80) REVERT: A 630 ASP cc_start: 0.8822 (m-30) cc_final: 0.8538 (m-30) REVERT: A 642 LEU cc_start: 0.9038 (mp) cc_final: 0.8670 (pt) REVERT: A 673 GLU cc_start: 0.8790 (pm20) cc_final: 0.8386 (pp20) REVERT: A 706 GLU cc_start: 0.9083 (tp30) cc_final: 0.8863 (tt0) REVERT: A 765 SER cc_start: 0.8985 (m) cc_final: 0.8297 (t) REVERT: B 244 TYR cc_start: 0.8770 (p90) cc_final: 0.8220 (p90) REVERT: B 315 LYS cc_start: 0.8632 (mmpt) cc_final: 0.8393 (mtpt) REVERT: B 316 THR cc_start: 0.8448 (p) cc_final: 0.8128 (p) REVERT: B 332 MET cc_start: 0.8610 (ppp) cc_final: 0.8322 (ppp) REVERT: B 388 MET cc_start: 0.8176 (ppp) cc_final: 0.7379 (ppp) REVERT: B 562 ILE cc_start: 0.9268 (mm) cc_final: 0.8977 (mm) REVERT: B 572 CYS cc_start: 0.5389 (p) cc_final: 0.5067 (p) REVERT: B 602 ASN cc_start: 0.8954 (m-40) cc_final: 0.8654 (m-40) REVERT: B 609 ASP cc_start: 0.8876 (t0) cc_final: 0.8507 (t0) REVERT: B 678 MET cc_start: 0.8765 (mtp) cc_final: 0.8295 (ptm) REVERT: B 736 PHE cc_start: 0.9104 (m-80) cc_final: 0.8822 (m-80) REVERT: C 306 LEU cc_start: 0.9089 (tp) cc_final: 0.8716 (tp) REVERT: C 349 ARG cc_start: 0.8527 (tpt90) cc_final: 0.8206 (tpt90) REVERT: C 384 HIS cc_start: 0.7543 (m90) cc_final: 0.7197 (m90) REVERT: C 388 MET cc_start: 0.8153 (ptp) cc_final: 0.6347 (ppp) REVERT: C 402 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7491 (pt0) REVERT: C 486 LYS cc_start: 0.7194 (tttt) cc_final: 0.6466 (tttt) REVERT: C 564 ASP cc_start: 0.9070 (t0) cc_final: 0.8724 (t0) REVERT: C 602 ASN cc_start: 0.8478 (m110) cc_final: 0.8173 (t0) REVERT: C 603 GLN cc_start: 0.9608 (tp-100) cc_final: 0.9246 (tp-100) REVERT: C 620 ILE cc_start: 0.9281 (mt) cc_final: 0.8992 (tp) REVERT: D 84 MET cc_start: 0.5966 (ptp) cc_final: 0.5589 (ptt) REVERT: D 132 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6725 (mp0) REVERT: D 306 LEU cc_start: 0.9418 (tp) cc_final: 0.9074 (tt) REVERT: D 314 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8643 (tm-30) REVERT: D 326 SER cc_start: 0.8975 (m) cc_final: 0.8738 (p) REVERT: D 332 MET cc_start: 0.7759 (tpt) cc_final: 0.7538 (tpp) REVERT: D 411 LEU cc_start: 0.9343 (mp) cc_final: 0.9074 (mp) REVERT: D 449 MET cc_start: 0.7834 (ptt) cc_final: 0.7012 (tmm) REVERT: D 538 ASN cc_start: 0.7791 (t0) cc_final: 0.7368 (t0) REVERT: D 602 ASN cc_start: 0.9062 (t0) cc_final: 0.8442 (t0) REVERT: D 653 ARG cc_start: 0.8222 (pmt170) cc_final: 0.7851 (ppt170) REVERT: D 757 MET cc_start: 0.7996 (ptt) cc_final: 0.7689 (ptp) REVERT: E 45 LYS cc_start: 0.8598 (tmmt) cc_final: 0.8388 (pttt) REVERT: E 84 MET cc_start: 0.3468 (ptt) cc_final: 0.3263 (ptt) REVERT: E 158 MET cc_start: 0.4986 (tmm) cc_final: 0.4423 (ptt) REVERT: E 366 GLU cc_start: 0.8121 (pm20) cc_final: 0.7885 (pm20) REVERT: E 427 MET cc_start: 0.8356 (ppp) cc_final: 0.7633 (ppp) REVERT: E 449 MET cc_start: 0.8209 (pmm) cc_final: 0.7935 (pmm) REVERT: E 564 ASP cc_start: 0.8923 (t0) cc_final: 0.8572 (t0) REVERT: E 567 ARG cc_start: 0.8934 (mtp180) cc_final: 0.8498 (mtm-85) REVERT: E 674 PHE cc_start: 0.8265 (t80) cc_final: 0.8049 (t80) REVERT: E 690 ILE cc_start: 0.8723 (mp) cc_final: 0.8097 (mp) REVERT: E 740 MET cc_start: 0.7022 (ptp) cc_final: 0.6794 (ptp) REVERT: F 52 PHE cc_start: 0.5884 (m-80) cc_final: 0.5319 (m-80) REVERT: F 194 GLU cc_start: 0.8500 (tt0) cc_final: 0.7581 (mp0) REVERT: F 205 ASP cc_start: 0.8508 (t0) cc_final: 0.8257 (t0) REVERT: F 315 LYS cc_start: 0.9538 (tptp) cc_final: 0.9241 (tptt) REVERT: F 354 ASP cc_start: 0.8631 (t70) cc_final: 0.8381 (t0) REVERT: F 397 GLU cc_start: 0.9221 (mp0) cc_final: 0.8951 (mp0) REVERT: F 470 GLU cc_start: 0.8855 (pm20) cc_final: 0.8448 (pm20) REVERT: F 508 MET cc_start: 0.7461 (mmm) cc_final: 0.7108 (mmm) REVERT: F 560 ARG cc_start: 0.8753 (mtt180) cc_final: 0.8447 (mtt-85) REVERT: F 564 ASP cc_start: 0.9393 (m-30) cc_final: 0.9153 (m-30) REVERT: F 577 ASP cc_start: 0.8230 (t0) cc_final: 0.7974 (t0) REVERT: F 578 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7664 (tm-30) REVERT: F 580 ASP cc_start: 0.8051 (m-30) cc_final: 0.7763 (m-30) REVERT: F 606 THR cc_start: 0.8610 (m) cc_final: 0.8407 (p) REVERT: F 607 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8789 (mm-30) REVERT: F 615 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8334 (mtmm) REVERT: F 630 ASP cc_start: 0.8706 (t0) cc_final: 0.8404 (t0) REVERT: I 332 MET cc_start: 0.3636 (mmp) cc_final: 0.3340 (mmm) REVERT: J 298 ILE cc_start: 0.6246 (tp) cc_final: 0.5416 (tp) REVERT: J 299 GLN cc_start: 0.4145 (mp10) cc_final: 0.3186 (tm-30) REVERT: J 365 ILE cc_start: 0.5711 (mt) cc_final: 0.5416 (mp) outliers start: 0 outliers final: 0 residues processed: 577 average time/residue: 0.2252 time to fit residues: 209.5823 Evaluate side-chains 447 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 338 optimal weight: 3.9990 chunk 399 optimal weight: 50.0000 chunk 346 optimal weight: 0.0040 chunk 309 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 302 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN C 327 GLN C 490 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN ** J 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.102034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.077236 restraints weight = 125185.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.078917 restraints weight = 84201.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.080204 restraints weight = 63663.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.080887 restraints weight = 51315.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.081616 restraints weight = 44828.589| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33789 Z= 0.163 Angle : 0.679 10.238 45698 Z= 0.350 Chirality : 0.046 0.227 5167 Planarity : 0.005 0.080 5980 Dihedral : 8.098 125.963 4666 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.77 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.13), residues: 4157 helix: 0.21 (0.13), residues: 1657 sheet: -1.38 (0.22), residues: 546 loop : -2.23 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 741 TYR 0.022 0.001 TYR A 495 PHE 0.029 0.002 PHE B 506 TRP 0.028 0.003 TRP C 551 HIS 0.006 0.001 HIS E 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (33789) covalent geometry : angle 0.67854 / 0.35 (45698) hydrogen bonds : bond 0.03429 / 2.30 ( 1175) hydrogen bonds : angle 5.25672 / 3.67 ( 3405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 545 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8177 (pm20) cc_final: 0.7819 (pm20) REVERT: A 312 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8762 (ttpp) REVERT: A 365 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8269 (mmt90) REVERT: A 379 GLU cc_start: 0.9433 (tt0) cc_final: 0.8806 (tp30) REVERT: A 397 GLU cc_start: 0.8670 (mp0) cc_final: 0.8047 (mp0) REVERT: A 561 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8875 (tm-30) REVERT: A 575 PHE cc_start: 0.8763 (t80) cc_final: 0.7914 (t80) REVERT: A 630 ASP cc_start: 0.8819 (m-30) cc_final: 0.8580 (m-30) REVERT: A 642 LEU cc_start: 0.9036 (mp) cc_final: 0.8705 (pt) REVERT: A 704 GLU cc_start: 0.9021 (tp30) cc_final: 0.8786 (tm-30) REVERT: A 765 SER cc_start: 0.8658 (m) cc_final: 0.8404 (t) REVERT: B 241 ILE cc_start: 0.9395 (mm) cc_final: 0.9150 (mm) REVERT: B 244 TYR cc_start: 0.8866 (p90) cc_final: 0.7988 (p90) REVERT: B 285 ASN cc_start: 0.8864 (t0) cc_final: 0.8616 (t0) REVERT: B 315 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8460 (mtpt) REVERT: B 316 THR cc_start: 0.8359 (p) cc_final: 0.8101 (p) REVERT: B 332 MET cc_start: 0.9014 (ppp) cc_final: 0.8638 (ppp) REVERT: B 388 MET cc_start: 0.8015 (ppp) cc_final: 0.7269 (ppp) REVERT: B 562 ILE cc_start: 0.9302 (mm) cc_final: 0.9031 (mm) REVERT: B 572 CYS cc_start: 0.5548 (p) cc_final: 0.5274 (p) REVERT: B 602 ASN cc_start: 0.8940 (m-40) cc_final: 0.8653 (m-40) REVERT: B 609 ASP cc_start: 0.8888 (t0) cc_final: 0.8540 (t0) REVERT: B 678 MET cc_start: 0.8757 (mtp) cc_final: 0.8491 (ptm) REVERT: B 736 PHE cc_start: 0.9102 (m-80) cc_final: 0.8856 (m-80) REVERT: C 292 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 349 ARG cc_start: 0.8571 (tpt90) cc_final: 0.8313 (tpt90) REVERT: C 402 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7864 (pt0) REVERT: C 564 ASP cc_start: 0.9114 (t0) cc_final: 0.8779 (t0) REVERT: C 602 ASN cc_start: 0.8489 (m110) cc_final: 0.8134 (t0) REVERT: C 603 GLN cc_start: 0.9611 (tp-100) cc_final: 0.9273 (tp-100) REVERT: C 620 ILE cc_start: 0.9375 (mt) cc_final: 0.9090 (tp) REVERT: C 695 CYS cc_start: 0.7993 (t) cc_final: 0.7743 (t) REVERT: D 84 MET cc_start: 0.5985 (ptp) cc_final: 0.5652 (ptt) REVERT: D 132 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6678 (mp0) REVERT: D 285 ASN cc_start: 0.8412 (m110) cc_final: 0.8158 (m-40) REVERT: D 291 GLU cc_start: 0.8688 (pt0) cc_final: 0.8409 (pp20) REVERT: D 306 LEU cc_start: 0.9417 (tp) cc_final: 0.9066 (tt) REVERT: D 314 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8726 (tm-30) REVERT: D 326 SER cc_start: 0.9067 (m) cc_final: 0.8844 (p) REVERT: D 332 MET cc_start: 0.8130 (tpt) cc_final: 0.7637 (tpp) REVERT: D 411 LEU cc_start: 0.9324 (mp) cc_final: 0.9086 (mp) REVERT: D 449 MET cc_start: 0.7956 (ptt) cc_final: 0.7078 (tmm) REVERT: D 538 ASN cc_start: 0.7879 (t0) cc_final: 0.7474 (t0) REVERT: D 602 ASN cc_start: 0.9087 (t0) cc_final: 0.8471 (t0) REVERT: D 653 ARG cc_start: 0.8431 (pmt170) cc_final: 0.8062 (ppt170) REVERT: D 757 MET cc_start: 0.8016 (ptt) cc_final: 0.7753 (ptp) REVERT: E 45 LYS cc_start: 0.8666 (tmmt) cc_final: 0.8448 (pttt) REVERT: E 158 MET cc_start: 0.4923 (tmm) cc_final: 0.4582 (ptt) REVERT: E 427 MET cc_start: 0.8471 (ppp) cc_final: 0.7702 (ppp) REVERT: E 449 MET cc_start: 0.8305 (pmm) cc_final: 0.8047 (pmm) REVERT: E 550 MET cc_start: 0.6936 (ttm) cc_final: 0.6692 (ttm) REVERT: E 564 ASP cc_start: 0.8933 (t0) cc_final: 0.8588 (t0) REVERT: E 567 ARG cc_start: 0.8966 (mtp180) cc_final: 0.8579 (mtm-85) REVERT: E 690 ILE cc_start: 0.8669 (mp) cc_final: 0.8039 (mp) REVERT: E 740 MET cc_start: 0.6948 (ptp) cc_final: 0.6727 (ptp) REVERT: F 52 PHE cc_start: 0.6144 (m-80) cc_final: 0.5441 (m-80) REVERT: F 194 GLU cc_start: 0.8499 (tt0) cc_final: 0.7579 (mp0) REVERT: F 205 ASP cc_start: 0.8629 (t0) cc_final: 0.8370 (t0) REVERT: F 238 PRO cc_start: 0.8499 (Cg_exo) cc_final: 0.8151 (Cg_endo) REVERT: F 244 TYR cc_start: 0.8359 (p90) cc_final: 0.7999 (p90) REVERT: F 305 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8200 (mt-10) REVERT: F 315 LYS cc_start: 0.9552 (tptp) cc_final: 0.9245 (tptt) REVERT: F 354 ASP cc_start: 0.8747 (t70) cc_final: 0.8469 (t0) REVERT: F 411 LEU cc_start: 0.9170 (tp) cc_final: 0.8965 (tp) REVERT: F 470 GLU cc_start: 0.8938 (pm20) cc_final: 0.8588 (pm20) REVERT: F 495 TYR cc_start: 0.8853 (m-80) cc_final: 0.8641 (m-80) REVERT: F 508 MET cc_start: 0.7492 (mmm) cc_final: 0.7146 (mmm) REVERT: F 560 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8340 (mtt-85) REVERT: F 564 ASP cc_start: 0.9409 (m-30) cc_final: 0.9158 (m-30) REVERT: F 577 ASP cc_start: 0.8412 (t0) cc_final: 0.8186 (t0) REVERT: F 606 THR cc_start: 0.8767 (m) cc_final: 0.8447 (p) REVERT: F 607 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8840 (mm-30) REVERT: F 630 ASP cc_start: 0.8767 (t0) cc_final: 0.8451 (t0) REVERT: I 332 MET cc_start: 0.3364 (mmp) cc_final: 0.3068 (mmm) outliers start: 1 outliers final: 1 residues processed: 546 average time/residue: 0.2220 time to fit residues: 195.3389 Evaluate side-chains 437 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 7 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 750 ASN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.100451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.076050 restraints weight = 126061.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.077707 restraints weight = 84000.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078914 restraints weight = 62588.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.079747 restraints weight = 50689.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.080381 restraints weight = 43772.783| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33789 Z= 0.185 Angle : 0.694 9.126 45698 Z= 0.361 Chirality : 0.047 0.217 5167 Planarity : 0.005 0.076 5980 Dihedral : 8.118 125.974 4666 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.13), residues: 4157 helix: 0.13 (0.13), residues: 1676 sheet: -1.38 (0.22), residues: 531 loop : -2.25 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 599 TYR 0.017 0.002 TYR A 495 PHE 0.041 0.002 PHE C 267 TRP 0.024 0.003 TRP E 551 HIS 0.007 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (33789) covalent geometry : angle 0.69403 / 0.36 (45698) hydrogen bonds : bond 0.03504 / 2.36 ( 1175) hydrogen bonds : angle 5.32652 / 3.70 ( 3405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8348 (pm20) cc_final: 0.7915 (pm20) REVERT: A 275 MET cc_start: 0.9198 (mmp) cc_final: 0.8959 (mmp) REVERT: A 312 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8802 (ttpp) REVERT: A 330 THR cc_start: 0.9212 (t) cc_final: 0.8893 (p) REVERT: A 365 ARG cc_start: 0.8478 (mmt180) cc_final: 0.8238 (mmt90) REVERT: A 379 GLU cc_start: 0.9493 (tt0) cc_final: 0.8914 (tp30) REVERT: A 397 GLU cc_start: 0.8807 (mp0) cc_final: 0.8191 (mp0) REVERT: A 442 MET cc_start: 0.7947 (mmp) cc_final: 0.7694 (mmt) REVERT: A 561 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8879 (tm-30) REVERT: A 575 PHE cc_start: 0.8934 (t80) cc_final: 0.8121 (t80) REVERT: A 630 ASP cc_start: 0.8865 (m-30) cc_final: 0.8470 (m-30) REVERT: A 642 LEU cc_start: 0.9109 (mp) cc_final: 0.8771 (pt) REVERT: A 765 SER cc_start: 0.8823 (m) cc_final: 0.8512 (t) REVERT: B 285 ASN cc_start: 0.9020 (t0) cc_final: 0.8736 (t0) REVERT: B 315 LYS cc_start: 0.8862 (mmpt) cc_final: 0.8559 (mtpt) REVERT: B 332 MET cc_start: 0.9135 (ppp) cc_final: 0.8635 (ppp) REVERT: B 381 LEU cc_start: 0.9412 (mt) cc_final: 0.9130 (mt) REVERT: B 388 MET cc_start: 0.8110 (ppp) cc_final: 0.7328 (ppp) REVERT: B 572 CYS cc_start: 0.5465 (p) cc_final: 0.5187 (p) REVERT: B 602 ASN cc_start: 0.8926 (m-40) cc_final: 0.8673 (m-40) REVERT: B 736 PHE cc_start: 0.9173 (m-80) cc_final: 0.8932 (m-80) REVERT: C 241 ILE cc_start: 0.9294 (mm) cc_final: 0.9092 (mm) REVERT: C 292 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8632 (tm-30) REVERT: C 344 MET cc_start: 0.8415 (tpp) cc_final: 0.8156 (tpp) REVERT: C 349 ARG cc_start: 0.8630 (tpt90) cc_final: 0.8322 (tpt90) REVERT: C 388 MET cc_start: 0.8277 (ptp) cc_final: 0.6533 (ppp) REVERT: C 402 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7741 (pt0) REVERT: C 560 ARG cc_start: 0.9319 (ttp-170) cc_final: 0.9106 (ttp80) REVERT: C 564 ASP cc_start: 0.9111 (t0) cc_final: 0.8809 (t0) REVERT: C 602 ASN cc_start: 0.8295 (m110) cc_final: 0.7860 (t0) REVERT: C 603 GLN cc_start: 0.9546 (tp-100) cc_final: 0.9260 (tp-100) REVERT: C 620 ILE cc_start: 0.9296 (mt) cc_final: 0.9010 (tp) REVERT: C 695 CYS cc_start: 0.8227 (t) cc_final: 0.7970 (t) REVERT: C 740 MET cc_start: 0.8266 (tmm) cc_final: 0.7942 (tmm) REVERT: D 291 GLU cc_start: 0.8728 (pt0) cc_final: 0.8387 (pp20) REVERT: D 306 LEU cc_start: 0.9439 (tp) cc_final: 0.9128 (tt) REVERT: D 326 SER cc_start: 0.9115 (m) cc_final: 0.8859 (p) REVERT: D 332 MET cc_start: 0.8157 (tpt) cc_final: 0.7592 (tpp) REVERT: D 411 LEU cc_start: 0.9353 (mp) cc_final: 0.9063 (mp) REVERT: D 449 MET cc_start: 0.8052 (ptt) cc_final: 0.7110 (tmm) REVERT: D 508 MET cc_start: 0.6009 (mmp) cc_final: 0.5770 (mmm) REVERT: D 538 ASN cc_start: 0.8144 (t0) cc_final: 0.7832 (t0) REVERT: D 602 ASN cc_start: 0.9082 (t0) cc_final: 0.8387 (t0) REVERT: D 653 ARG cc_start: 0.8570 (pmt170) cc_final: 0.8178 (ppt170) REVERT: E 84 MET cc_start: 0.3627 (ptt) cc_final: 0.3384 (ptt) REVERT: E 110 TYR cc_start: 0.6549 (m-10) cc_final: 0.6178 (t80) REVERT: E 158 MET cc_start: 0.5249 (tmm) cc_final: 0.4738 (ptt) REVERT: E 348 ASN cc_start: 0.9096 (m-40) cc_final: 0.8666 (t0) REVERT: E 427 MET cc_start: 0.8440 (ppp) cc_final: 0.7665 (ppp) REVERT: E 449 MET cc_start: 0.8416 (pmm) cc_final: 0.8129 (pmm) REVERT: E 550 MET cc_start: 0.7337 (ttm) cc_final: 0.6867 (ttm) REVERT: E 564 ASP cc_start: 0.8951 (t0) cc_final: 0.8598 (t0) REVERT: E 567 ARG cc_start: 0.9023 (mtp180) cc_final: 0.8615 (mtm-85) REVERT: F 52 PHE cc_start: 0.6244 (m-80) cc_final: 0.5515 (m-80) REVERT: F 194 GLU cc_start: 0.8515 (tt0) cc_final: 0.7597 (mp0) REVERT: F 205 ASP cc_start: 0.8681 (t0) cc_final: 0.8474 (t0) REVERT: F 315 LYS cc_start: 0.9612 (tptp) cc_final: 0.9295 (tptt) REVERT: F 354 ASP cc_start: 0.8726 (t70) cc_final: 0.8460 (t0) REVERT: F 495 TYR cc_start: 0.8961 (m-80) cc_final: 0.8674 (m-80) REVERT: F 508 MET cc_start: 0.7605 (mmm) cc_final: 0.7343 (mmm) REVERT: F 560 ARG cc_start: 0.8805 (mtt180) cc_final: 0.8321 (mtt-85) REVERT: F 564 ASP cc_start: 0.9447 (m-30) cc_final: 0.9200 (m-30) REVERT: F 577 ASP cc_start: 0.8397 (t0) cc_final: 0.8126 (t0) REVERT: F 606 THR cc_start: 0.8792 (m) cc_final: 0.8375 (p) REVERT: F 607 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8872 (mm-30) REVERT: F 630 ASP cc_start: 0.8853 (t0) cc_final: 0.8544 (t0) REVERT: I 332 MET cc_start: 0.3456 (mmp) cc_final: 0.3142 (mmm) outliers start: 2 outliers final: 0 residues processed: 545 average time/residue: 0.2270 time to fit residues: 199.8519 Evaluate side-chains 416 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 262 optimal weight: 8.9990 chunk 10 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 chunk 379 optimal weight: 0.8980 chunk 338 optimal weight: 0.0270 chunk 215 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 384 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 602 ASN A 603 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.101552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.076887 restraints weight = 125349.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.078615 restraints weight = 83917.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.079791 restraints weight = 63117.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.080684 restraints weight = 51605.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.081264 restraints weight = 44050.958| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33789 Z= 0.144 Angle : 0.676 10.756 45698 Z= 0.348 Chirality : 0.047 0.276 5167 Planarity : 0.005 0.072 5980 Dihedral : 8.048 124.752 4666 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.13), residues: 4157 helix: 0.23 (0.13), residues: 1665 sheet: -1.41 (0.22), residues: 523 loop : -2.19 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 64 TYR 0.026 0.001 TYR E 495 PHE 0.031 0.002 PHE B 506 TRP 0.021 0.002 TRP E 551 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (33789) covalent geometry : angle 0.67567 / 0.35 (45698) hydrogen bonds : bond 0.03301 / 2.22 ( 1175) hydrogen bonds : angle 5.17396 / 3.60 ( 3405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 546 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9006 (mmp) cc_final: 0.8791 (mmp) REVERT: A 312 LYS cc_start: 0.9240 (ttpp) cc_final: 0.8763 (ttpp) REVERT: A 330 THR cc_start: 0.9145 (t) cc_final: 0.8837 (p) REVERT: A 349 ARG cc_start: 0.8823 (ptp-170) cc_final: 0.8622 (ptp-170) REVERT: A 365 ARG cc_start: 0.8394 (mmt180) cc_final: 0.8179 (mmt90) REVERT: A 379 GLU cc_start: 0.9461 (tt0) cc_final: 0.8858 (tp30) REVERT: A 561 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8864 (tm-30) REVERT: A 575 PHE cc_start: 0.8856 (t80) cc_final: 0.7961 (t80) REVERT: A 630 ASP cc_start: 0.8937 (m-30) cc_final: 0.8694 (m-30) REVERT: A 634 LEU cc_start: 0.8418 (tt) cc_final: 0.8060 (tt) REVERT: A 642 LEU cc_start: 0.9131 (mp) cc_final: 0.8657 (pt) REVERT: A 764 GLN cc_start: 0.8513 (mt0) cc_final: 0.7853 (mp10) REVERT: A 765 SER cc_start: 0.8628 (m) cc_final: 0.8301 (t) REVERT: B 285 ASN cc_start: 0.8888 (t0) cc_final: 0.8647 (t0) REVERT: B 315 LYS cc_start: 0.8975 (mmpt) cc_final: 0.8704 (mtpt) REVERT: B 332 MET cc_start: 0.9083 (ppp) cc_final: 0.8583 (ppp) REVERT: B 381 LEU cc_start: 0.9389 (mt) cc_final: 0.9133 (mt) REVERT: B 388 MET cc_start: 0.8139 (ppp) cc_final: 0.7261 (ppp) REVERT: B 578 GLU cc_start: 0.8921 (tp30) cc_final: 0.8490 (tp30) REVERT: B 602 ASN cc_start: 0.8893 (m-40) cc_final: 0.8610 (m-40) REVERT: B 609 ASP cc_start: 0.8823 (t0) cc_final: 0.8492 (t0) REVERT: B 736 PHE cc_start: 0.9111 (m-80) cc_final: 0.8893 (m-80) REVERT: C 241 ILE cc_start: 0.9259 (mm) cc_final: 0.9034 (mm) REVERT: C 292 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8590 (tm-30) REVERT: C 388 MET cc_start: 0.8179 (ptp) cc_final: 0.6384 (ppp) REVERT: C 402 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7704 (pt0) REVERT: C 558 ASN cc_start: 0.8357 (p0) cc_final: 0.8030 (p0) REVERT: C 559 VAL cc_start: 0.9114 (t) cc_final: 0.8893 (t) REVERT: C 560 ARG cc_start: 0.9293 (ttp-170) cc_final: 0.8899 (tpp80) REVERT: C 564 ASP cc_start: 0.9083 (t0) cc_final: 0.8759 (t0) REVERT: C 602 ASN cc_start: 0.8406 (m110) cc_final: 0.7966 (t0) REVERT: C 603 GLN cc_start: 0.9550 (tp-100) cc_final: 0.9212 (tp-100) REVERT: C 620 ILE cc_start: 0.9308 (mt) cc_final: 0.9037 (tp) REVERT: C 695 CYS cc_start: 0.7947 (t) cc_final: 0.7657 (t) REVERT: D 291 GLU cc_start: 0.8651 (pt0) cc_final: 0.8345 (pp20) REVERT: D 306 LEU cc_start: 0.9405 (tp) cc_final: 0.9127 (tt) REVERT: D 314 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8651 (tm-30) REVERT: D 326 SER cc_start: 0.9103 (m) cc_final: 0.8875 (p) REVERT: D 332 MET cc_start: 0.7939 (tpt) cc_final: 0.7614 (tpp) REVERT: D 344 MET cc_start: 0.7909 (mpp) cc_final: 0.7557 (mpp) REVERT: D 411 LEU cc_start: 0.9302 (mp) cc_final: 0.9080 (mp) REVERT: D 449 MET cc_start: 0.7975 (ptt) cc_final: 0.7039 (tmm) REVERT: D 538 ASN cc_start: 0.8012 (t0) cc_final: 0.7719 (t0) REVERT: D 602 ASN cc_start: 0.9097 (t0) cc_final: 0.8470 (t0) REVERT: D 653 ARG cc_start: 0.8358 (pmt170) cc_final: 0.8017 (ppt170) REVERT: E 84 MET cc_start: 0.3798 (ptt) cc_final: 0.3572 (ptt) REVERT: E 110 TYR cc_start: 0.6580 (m-10) cc_final: 0.6201 (t80) REVERT: E 158 MET cc_start: 0.5235 (tmm) cc_final: 0.4705 (ptt) REVERT: E 348 ASN cc_start: 0.9161 (m-40) cc_final: 0.8712 (t0) REVERT: E 366 GLU cc_start: 0.8193 (pm20) cc_final: 0.7810 (pm20) REVERT: E 427 MET cc_start: 0.8449 (ppp) cc_final: 0.7679 (ppp) REVERT: E 449 MET cc_start: 0.8327 (pmm) cc_final: 0.8052 (pmm) REVERT: E 546 GLU cc_start: 0.9447 (tp30) cc_final: 0.9230 (tp30) REVERT: E 564 ASP cc_start: 0.8901 (t0) cc_final: 0.8594 (t70) REVERT: E 567 ARG cc_start: 0.9007 (mtp180) cc_final: 0.8584 (mtm-85) REVERT: E 690 ILE cc_start: 0.8704 (mp) cc_final: 0.8159 (mp) REVERT: F 52 PHE cc_start: 0.6199 (m-80) cc_final: 0.5469 (m-80) REVERT: F 194 GLU cc_start: 0.8458 (tt0) cc_final: 0.8104 (tt0) REVERT: F 251 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8545 (mttp) REVERT: F 315 LYS cc_start: 0.9571 (tptp) cc_final: 0.9231 (tptt) REVERT: F 354 ASP cc_start: 0.8630 (t70) cc_final: 0.8374 (t0) REVERT: F 466 GLU cc_start: 0.8289 (mp0) cc_final: 0.8056 (pp20) REVERT: F 508 MET cc_start: 0.7494 (mmm) cc_final: 0.7236 (mmm) REVERT: F 560 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8311 (mtt-85) REVERT: F 564 ASP cc_start: 0.9415 (m-30) cc_final: 0.9162 (m-30) REVERT: F 577 ASP cc_start: 0.8865 (t0) cc_final: 0.8603 (t70) REVERT: F 580 ASP cc_start: 0.8350 (m-30) cc_final: 0.8135 (m-30) REVERT: F 602 ASN cc_start: 0.8859 (m110) cc_final: 0.8052 (t0) REVERT: F 606 THR cc_start: 0.8898 (m) cc_final: 0.8501 (p) REVERT: F 607 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8851 (mm-30) REVERT: F 630 ASP cc_start: 0.8822 (t0) cc_final: 0.8505 (t0) REVERT: I 332 MET cc_start: 0.3433 (mmp) cc_final: 0.3115 (mmm) outliers start: 1 outliers final: 0 residues processed: 546 average time/residue: 0.2229 time to fit residues: 196.6832 Evaluate side-chains 426 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 301 optimal weight: 0.9980 chunk 228 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 360 optimal weight: 0.9980 chunk 237 optimal weight: 0.0060 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.102167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.077599 restraints weight = 124429.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.079117 restraints weight = 82985.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.080475 restraints weight = 63254.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.081362 restraints weight = 50989.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.081988 restraints weight = 43884.350| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33789 Z= 0.134 Angle : 0.684 13.347 45698 Z= 0.350 Chirality : 0.046 0.252 5167 Planarity : 0.005 0.072 5980 Dihedral : 7.972 123.677 4666 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.03 % Allowed : 1.42 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 4157 helix: 0.23 (0.13), residues: 1670 sheet: -1.36 (0.22), residues: 526 loop : -2.14 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B 711 TYR 0.015 0.001 TYR F 173 PHE 0.032 0.001 PHE B 506 TRP 0.024 0.002 TRP E 551 HIS 0.006 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (33789) covalent geometry : angle 0.68398 / 0.35 (45698) hydrogen bonds : bond 0.03215 / 2.15 ( 1175) hydrogen bonds : angle 5.14854 / 3.58 ( 3405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 546 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 THR cc_start: 0.9057 (t) cc_final: 0.8637 (p) REVERT: A 379 GLU cc_start: 0.9453 (tt0) cc_final: 0.8844 (tp30) REVERT: A 561 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8751 (tm-30) REVERT: A 575 PHE cc_start: 0.8858 (t80) cc_final: 0.8466 (t80) REVERT: A 602 ASN cc_start: 0.8725 (m-40) cc_final: 0.8287 (t0) REVERT: A 630 ASP cc_start: 0.9001 (m-30) cc_final: 0.8745 (m-30) REVERT: A 634 LEU cc_start: 0.8561 (tt) cc_final: 0.8219 (tt) REVERT: A 642 LEU cc_start: 0.9153 (mp) cc_final: 0.8715 (pt) REVERT: A 764 GLN cc_start: 0.8596 (mt0) cc_final: 0.7875 (mp10) REVERT: A 765 SER cc_start: 0.8681 (m) cc_final: 0.8340 (t) REVERT: B 315 LYS cc_start: 0.8872 (mmpt) cc_final: 0.8665 (mtpt) REVERT: B 332 MET cc_start: 0.9104 (ppp) cc_final: 0.8598 (ppp) REVERT: B 381 LEU cc_start: 0.9376 (mt) cc_final: 0.9108 (mt) REVERT: B 388 MET cc_start: 0.8171 (ppp) cc_final: 0.7282 (ppp) REVERT: B 578 GLU cc_start: 0.9005 (tp30) cc_final: 0.8482 (tp30) REVERT: B 602 ASN cc_start: 0.8875 (m-40) cc_final: 0.8625 (m-40) REVERT: B 609 ASP cc_start: 0.8819 (t0) cc_final: 0.8511 (t0) REVERT: B 678 MET cc_start: 0.8894 (mtp) cc_final: 0.8570 (ptm) REVERT: B 736 PHE cc_start: 0.9092 (m-80) cc_final: 0.8877 (m-80) REVERT: C 292 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8331 (tm-30) REVERT: C 388 MET cc_start: 0.8172 (ptp) cc_final: 0.6449 (ppp) REVERT: C 402 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7687 (pt0) REVERT: C 560 ARG cc_start: 0.9371 (ttp-170) cc_final: 0.9021 (tpp80) REVERT: C 561 GLU cc_start: 0.8915 (pm20) cc_final: 0.8606 (pm20) REVERT: C 564 ASP cc_start: 0.9067 (t0) cc_final: 0.8759 (t0) REVERT: C 578 GLU cc_start: 0.8879 (tt0) cc_final: 0.8661 (tt0) REVERT: C 602 ASN cc_start: 0.8305 (m110) cc_final: 0.7863 (t0) REVERT: C 603 GLN cc_start: 0.9530 (tp-100) cc_final: 0.9199 (tp-100) REVERT: C 620 ILE cc_start: 0.9295 (mt) cc_final: 0.9042 (tp) REVERT: D 291 GLU cc_start: 0.8664 (pt0) cc_final: 0.8423 (pp20) REVERT: D 306 LEU cc_start: 0.9431 (tp) cc_final: 0.9020 (tt) REVERT: D 314 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8655 (tm-30) REVERT: D 326 SER cc_start: 0.9082 (m) cc_final: 0.8847 (p) REVERT: D 332 MET cc_start: 0.7803 (tpt) cc_final: 0.7291 (tpp) REVERT: D 366 GLU cc_start: 0.8051 (mp0) cc_final: 0.7815 (mp0) REVERT: D 449 MET cc_start: 0.7971 (ptt) cc_final: 0.6963 (tmm) REVERT: D 538 ASN cc_start: 0.8085 (t0) cc_final: 0.7784 (t0) REVERT: D 602 ASN cc_start: 0.8723 (t0) cc_final: 0.8515 (t0) REVERT: D 603 GLN cc_start: 0.9181 (tt0) cc_final: 0.8772 (pt0) REVERT: D 653 ARG cc_start: 0.8405 (pmt170) cc_final: 0.8011 (ppt170) REVERT: E 158 MET cc_start: 0.5054 (tmm) cc_final: 0.4661 (ptt) REVERT: E 302 PHE cc_start: 0.8304 (t80) cc_final: 0.7671 (t80) REVERT: E 348 ASN cc_start: 0.9147 (m-40) cc_final: 0.8715 (t0) REVERT: E 427 MET cc_start: 0.8441 (ppp) cc_final: 0.7656 (ppp) REVERT: E 449 MET cc_start: 0.8355 (pmm) cc_final: 0.8067 (pmm) REVERT: E 508 MET cc_start: 0.6045 (ttt) cc_final: 0.5513 (tmm) REVERT: E 564 ASP cc_start: 0.8909 (t0) cc_final: 0.8613 (t70) REVERT: E 567 ARG cc_start: 0.8988 (mtp180) cc_final: 0.8564 (mtm-85) REVERT: E 690 ILE cc_start: 0.8711 (mp) cc_final: 0.8062 (mp) REVERT: F 52 PHE cc_start: 0.6167 (m-80) cc_final: 0.5466 (m-80) REVERT: F 194 GLU cc_start: 0.8436 (tt0) cc_final: 0.8061 (tt0) REVERT: F 251 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8547 (mttp) REVERT: F 315 LYS cc_start: 0.9590 (tptp) cc_final: 0.9213 (tptt) REVERT: F 354 ASP cc_start: 0.8569 (t70) cc_final: 0.8301 (t0) REVERT: F 508 MET cc_start: 0.7481 (mmm) cc_final: 0.7200 (mmm) REVERT: F 560 ARG cc_start: 0.8766 (mtt180) cc_final: 0.8326 (mtt-85) REVERT: F 564 ASP cc_start: 0.9426 (m-30) cc_final: 0.9171 (m-30) REVERT: F 577 ASP cc_start: 0.8863 (t0) cc_final: 0.8620 (t70) REVERT: F 602 ASN cc_start: 0.8803 (m110) cc_final: 0.8415 (p0) REVERT: F 604 ILE cc_start: 0.9458 (pt) cc_final: 0.9228 (pt) REVERT: F 606 THR cc_start: 0.8833 (m) cc_final: 0.8526 (p) REVERT: F 607 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8866 (mm-30) REVERT: F 630 ASP cc_start: 0.8818 (t0) cc_final: 0.8477 (t0) REVERT: I 332 MET cc_start: 0.3429 (mmp) cc_final: 0.3131 (mmm) outliers start: 1 outliers final: 0 residues processed: 546 average time/residue: 0.2165 time to fit residues: 191.8098 Evaluate side-chains 422 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 368 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 401 optimal weight: 30.0000 chunk 182 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 404 optimal weight: 0.3980 chunk 239 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.100266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.075814 restraints weight = 126853.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.077490 restraints weight = 84392.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.078831 restraints weight = 63454.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.079704 restraints weight = 51333.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.080282 restraints weight = 44199.625| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33789 Z= 0.175 Angle : 0.716 11.179 45698 Z= 0.368 Chirality : 0.047 0.234 5167 Planarity : 0.005 0.072 5980 Dihedral : 8.012 124.178 4666 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 4157 helix: 0.15 (0.13), residues: 1678 sheet: -1.37 (0.22), residues: 533 loop : -2.20 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 711 TYR 0.016 0.001 TYR F 244 PHE 0.030 0.002 PHE B 506 TRP 0.036 0.003 TRP C 551 HIS 0.006 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (33789) covalent geometry : angle 0.71592 / 0.37 (45698) hydrogen bonds : bond 0.03400 / 2.25 ( 1175) hydrogen bonds : angle 5.26761 / 3.66 ( 3405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 THR cc_start: 0.9179 (t) cc_final: 0.8897 (p) REVERT: A 379 GLU cc_start: 0.9475 (tt0) cc_final: 0.8932 (tp30) REVERT: A 442 MET cc_start: 0.7780 (mmp) cc_final: 0.7524 (mmt) REVERT: A 470 GLU cc_start: 0.8559 (mp0) cc_final: 0.8285 (mp0) REVERT: A 561 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8758 (tm-30) REVERT: A 602 ASN cc_start: 0.9145 (m-40) cc_final: 0.8929 (m-40) REVERT: A 609 ASP cc_start: 0.9327 (t0) cc_final: 0.8925 (p0) REVERT: A 630 ASP cc_start: 0.8965 (m-30) cc_final: 0.8702 (m-30) REVERT: A 634 LEU cc_start: 0.8622 (tt) cc_final: 0.8120 (tt) REVERT: A 642 LEU cc_start: 0.9161 (mp) cc_final: 0.8729 (pt) REVERT: A 764 GLN cc_start: 0.8362 (mt0) cc_final: 0.7756 (mp10) REVERT: A 765 SER cc_start: 0.8791 (m) cc_final: 0.8387 (t) REVERT: B 292 GLU cc_start: 0.8034 (pt0) cc_final: 0.7562 (pp20) REVERT: B 316 THR cc_start: 0.8065 (p) cc_final: 0.7843 (p) REVERT: B 332 MET cc_start: 0.9116 (ppp) cc_final: 0.8586 (ppp) REVERT: B 381 LEU cc_start: 0.9416 (mt) cc_final: 0.9167 (mt) REVERT: B 388 MET cc_start: 0.8223 (ppp) cc_final: 0.7312 (ppp) REVERT: B 572 CYS cc_start: 0.5358 (p) cc_final: 0.5135 (p) REVERT: B 578 GLU cc_start: 0.9025 (tp30) cc_final: 0.8500 (tp30) REVERT: B 602 ASN cc_start: 0.9082 (m-40) cc_final: 0.8836 (m-40) REVERT: B 609 ASP cc_start: 0.8815 (t0) cc_final: 0.8531 (t0) REVERT: C 241 ILE cc_start: 0.9221 (mm) cc_final: 0.8983 (mm) REVERT: C 292 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8364 (tm-30) REVERT: C 388 MET cc_start: 0.7980 (ptp) cc_final: 0.6197 (ppp) REVERT: C 402 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7894 (pt0) REVERT: C 417 GLU cc_start: 0.8620 (tp30) cc_final: 0.8400 (tp30) REVERT: C 486 LYS cc_start: 0.6997 (tttt) cc_final: 0.6772 (tttm) REVERT: C 560 ARG cc_start: 0.9393 (ttp-170) cc_final: 0.9091 (tpp80) REVERT: C 564 ASP cc_start: 0.9092 (t0) cc_final: 0.8795 (t0) REVERT: C 578 GLU cc_start: 0.8948 (tt0) cc_final: 0.8730 (tt0) REVERT: C 602 ASN cc_start: 0.8403 (m110) cc_final: 0.7973 (t0) REVERT: C 603 GLN cc_start: 0.9540 (tp-100) cc_final: 0.9248 (tp-100) REVERT: C 620 ILE cc_start: 0.9315 (mt) cc_final: 0.9045 (tp) REVERT: D 84 MET cc_start: 0.3903 (ttp) cc_final: 0.3506 (ppp) REVERT: D 291 GLU cc_start: 0.8594 (pt0) cc_final: 0.8347 (pp20) REVERT: D 306 LEU cc_start: 0.9430 (tp) cc_final: 0.9162 (tt) REVERT: D 314 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8651 (tm-30) REVERT: D 326 SER cc_start: 0.9116 (m) cc_final: 0.8907 (p) REVERT: D 332 MET cc_start: 0.7877 (tpt) cc_final: 0.7282 (tpp) REVERT: D 449 MET cc_start: 0.8036 (ptt) cc_final: 0.7086 (tmm) REVERT: D 538 ASN cc_start: 0.8057 (t0) cc_final: 0.7756 (t0) REVERT: D 602 ASN cc_start: 0.8733 (t0) cc_final: 0.8479 (t0) REVERT: D 653 ARG cc_start: 0.8602 (pmt170) cc_final: 0.8192 (ppt170) REVERT: D 757 MET cc_start: 0.8174 (ptt) cc_final: 0.7808 (ptt) REVERT: E 84 MET cc_start: 0.3790 (ptt) cc_final: 0.3562 (ptt) REVERT: E 158 MET cc_start: 0.4933 (tmm) cc_final: 0.4469 (ptt) REVERT: E 348 ASN cc_start: 0.9182 (m-40) cc_final: 0.8743 (t0) REVERT: E 427 MET cc_start: 0.8488 (ppp) cc_final: 0.7682 (ppp) REVERT: E 449 MET cc_start: 0.8351 (pmm) cc_final: 0.8090 (pmm) REVERT: E 508 MET cc_start: 0.6322 (ttt) cc_final: 0.5535 (tmm) REVERT: E 550 MET cc_start: 0.6520 (ttm) cc_final: 0.5957 (ttm) REVERT: E 564 ASP cc_start: 0.8942 (t0) cc_final: 0.8627 (t70) REVERT: E 567 ARG cc_start: 0.8980 (mtp180) cc_final: 0.8554 (mtm-85) REVERT: F 52 PHE cc_start: 0.6279 (m-80) cc_final: 0.5551 (m-80) REVERT: F 194 GLU cc_start: 0.8363 (tt0) cc_final: 0.7982 (tt0) REVERT: F 244 TYR cc_start: 0.7934 (p90) cc_final: 0.7286 (p90) REVERT: F 251 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8484 (mttp) REVERT: F 315 LYS cc_start: 0.9585 (tptp) cc_final: 0.9219 (tptt) REVERT: F 332 MET cc_start: 0.9086 (tpp) cc_final: 0.8755 (tpp) REVERT: F 354 ASP cc_start: 0.8592 (t70) cc_final: 0.8325 (t0) REVERT: F 466 GLU cc_start: 0.8355 (mp0) cc_final: 0.7932 (pp20) REVERT: F 470 GLU cc_start: 0.8716 (pm20) cc_final: 0.8418 (pm20) REVERT: F 495 TYR cc_start: 0.8952 (m-80) cc_final: 0.8712 (m-80) REVERT: F 508 MET cc_start: 0.7553 (mmm) cc_final: 0.7318 (mmm) REVERT: F 560 ARG cc_start: 0.8745 (mtt180) cc_final: 0.8309 (mtt-85) REVERT: F 564 ASP cc_start: 0.9429 (m-30) cc_final: 0.9116 (m-30) REVERT: F 567 ARG cc_start: 0.9298 (mmm-85) cc_final: 0.8957 (mmt-90) REVERT: F 577 ASP cc_start: 0.8717 (t0) cc_final: 0.8423 (t70) REVERT: F 602 ASN cc_start: 0.8915 (m110) cc_final: 0.8474 (p0) REVERT: F 606 THR cc_start: 0.8899 (m) cc_final: 0.8556 (p) REVERT: F 607 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8934 (mm-30) REVERT: F 630 ASP cc_start: 0.8783 (t0) cc_final: 0.8469 (t0) REVERT: I 332 MET cc_start: 0.3381 (mmp) cc_final: 0.3065 (mmm) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.2206 time to fit residues: 188.8422 Evaluate side-chains 415 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 337 optimal weight: 20.0000 chunk 380 optimal weight: 0.0980 chunk 7 optimal weight: 20.0000 chunk 375 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 411 optimal weight: 20.0000 chunk 365 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 602 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.100985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.075986 restraints weight = 128057.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077791 restraints weight = 85865.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.079056 restraints weight = 64766.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.079903 restraints weight = 52293.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.080483 restraints weight = 44728.893| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33789 Z= 0.148 Angle : 0.700 11.051 45698 Z= 0.360 Chirality : 0.047 0.231 5167 Planarity : 0.005 0.072 5980 Dihedral : 7.964 122.206 4666 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.19 % Favored : 90.79 % Rotamer: Outliers : 0.03 % Allowed : 0.59 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.13), residues: 4157 helix: 0.20 (0.13), residues: 1670 sheet: -1.29 (0.22), residues: 518 loop : -2.16 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 711 TYR 0.016 0.001 TYR F 244 PHE 0.031 0.002 PHE B 506 TRP 0.037 0.003 TRP C 551 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (33789) covalent geometry : angle 0.69969 / 0.36 (45698) hydrogen bonds : bond 0.03274 / 2.18 ( 1175) hydrogen bonds : angle 5.24211 / 3.62 ( 3405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 531 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLU cc_start: 0.9511 (tt0) cc_final: 0.8926 (tp30) REVERT: A 397 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8722 (mm-30) REVERT: A 561 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8734 (tm-30) REVERT: A 575 PHE cc_start: 0.8828 (t80) cc_final: 0.8460 (t80) REVERT: A 609 ASP cc_start: 0.9330 (t0) cc_final: 0.8930 (p0) REVERT: A 630 ASP cc_start: 0.8949 (m-30) cc_final: 0.8736 (m-30) REVERT: A 634 LEU cc_start: 0.8562 (tt) cc_final: 0.8084 (tt) REVERT: A 642 LEU cc_start: 0.9122 (mp) cc_final: 0.8728 (pt) REVERT: A 764 GLN cc_start: 0.8333 (mt0) cc_final: 0.7783 (mp10) REVERT: A 765 SER cc_start: 0.8812 (m) cc_final: 0.8399 (t) REVERT: B 285 ASN cc_start: 0.8864 (t0) cc_final: 0.8663 (t0) REVERT: B 292 GLU cc_start: 0.8027 (pt0) cc_final: 0.7780 (pp20) REVERT: B 332 MET cc_start: 0.9097 (ppp) cc_final: 0.8665 (ppp) REVERT: B 388 MET cc_start: 0.8282 (ppp) cc_final: 0.7324 (ppp) REVERT: B 508 MET cc_start: 0.6404 (mmt) cc_final: 0.5196 (mmt) REVERT: B 578 GLU cc_start: 0.9041 (tp30) cc_final: 0.8520 (tp30) REVERT: B 602 ASN cc_start: 0.9130 (m-40) cc_final: 0.8922 (m-40) REVERT: C 236 LYS cc_start: 0.7662 (mmpt) cc_final: 0.6969 (mmmt) REVERT: C 241 ILE cc_start: 0.9235 (mm) cc_final: 0.9006 (mm) REVERT: C 281 GLU cc_start: 0.8252 (mp0) cc_final: 0.7689 (mp0) REVERT: C 388 MET cc_start: 0.8186 (ptp) cc_final: 0.6488 (ppp) REVERT: C 402 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7789 (pt0) REVERT: C 486 LYS cc_start: 0.7129 (tttt) cc_final: 0.6802 (tttm) REVERT: C 560 ARG cc_start: 0.9392 (ttp-170) cc_final: 0.9044 (tpp80) REVERT: C 564 ASP cc_start: 0.9071 (t0) cc_final: 0.8770 (t0) REVERT: C 578 GLU cc_start: 0.8931 (tt0) cc_final: 0.8718 (tt0) REVERT: C 602 ASN cc_start: 0.8312 (m110) cc_final: 0.7860 (t0) REVERT: C 603 GLN cc_start: 0.9528 (tp-100) cc_final: 0.9254 (tp-100) REVERT: C 620 ILE cc_start: 0.9311 (mt) cc_final: 0.9058 (tp) REVERT: C 740 MET cc_start: 0.8063 (tmm) cc_final: 0.7831 (tmm) REVERT: D 89 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6577 (tmm-80) REVERT: D 239 ARG cc_start: 0.7740 (ptm160) cc_final: 0.7408 (ptt180) REVERT: D 291 GLU cc_start: 0.8562 (pt0) cc_final: 0.8299 (pp20) REVERT: D 306 LEU cc_start: 0.9428 (tp) cc_final: 0.9045 (tt) REVERT: D 314 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8635 (tm-30) REVERT: D 326 SER cc_start: 0.9090 (m) cc_final: 0.8885 (p) REVERT: D 366 GLU cc_start: 0.8368 (mp0) cc_final: 0.8040 (mp0) REVERT: D 449 MET cc_start: 0.8028 (ptt) cc_final: 0.6977 (tmm) REVERT: D 602 ASN cc_start: 0.8737 (t0) cc_final: 0.8482 (t0) REVERT: D 653 ARG cc_start: 0.8497 (pmt170) cc_final: 0.8179 (ppt170) REVERT: D 757 MET cc_start: 0.8130 (ptt) cc_final: 0.7737 (ptt) REVERT: E 158 MET cc_start: 0.5367 (tmm) cc_final: 0.5001 (ptt) REVERT: E 219 MET cc_start: 0.9027 (mmt) cc_final: 0.8750 (mmm) REVERT: E 242 LEU cc_start: 0.9230 (mp) cc_final: 0.9030 (mp) REVERT: E 302 PHE cc_start: 0.8329 (t80) cc_final: 0.7696 (t80) REVERT: E 348 ASN cc_start: 0.9201 (m-40) cc_final: 0.8826 (t0) REVERT: E 366 GLU cc_start: 0.6904 (mp0) cc_final: 0.6641 (mp0) REVERT: E 427 MET cc_start: 0.8503 (ppp) cc_final: 0.8142 (ppp) REVERT: E 449 MET cc_start: 0.8338 (pmm) cc_final: 0.8052 (pmm) REVERT: E 550 MET cc_start: 0.6853 (ttm) cc_final: 0.6626 (ttm) REVERT: E 564 ASP cc_start: 0.8923 (t0) cc_final: 0.8615 (t70) REVERT: E 567 ARG cc_start: 0.8975 (mtp180) cc_final: 0.8546 (mtm-85) REVERT: F 52 PHE cc_start: 0.6224 (m-80) cc_final: 0.5540 (m-80) REVERT: F 143 TYR cc_start: 0.7092 (m-10) cc_final: 0.6817 (m-10) REVERT: F 194 GLU cc_start: 0.8435 (tt0) cc_final: 0.8061 (tt0) REVERT: F 244 TYR cc_start: 0.7904 (p90) cc_final: 0.7298 (p90) REVERT: F 251 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8578 (mttp) REVERT: F 315 LYS cc_start: 0.9618 (tptp) cc_final: 0.9298 (tptt) REVERT: F 332 MET cc_start: 0.9045 (tpp) cc_final: 0.8674 (tpp) REVERT: F 354 ASP cc_start: 0.8574 (t70) cc_final: 0.8310 (t0) REVERT: F 495 TYR cc_start: 0.8940 (m-80) cc_final: 0.8699 (m-80) REVERT: F 508 MET cc_start: 0.7295 (mmm) cc_final: 0.6978 (mmm) REVERT: F 560 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8210 (mtt-85) REVERT: F 564 ASP cc_start: 0.9426 (m-30) cc_final: 0.9137 (m-30) REVERT: F 567 ARG cc_start: 0.9297 (mmm-85) cc_final: 0.9047 (mmt-90) REVERT: F 577 ASP cc_start: 0.8721 (t0) cc_final: 0.8431 (t70) REVERT: F 602 ASN cc_start: 0.8945 (m110) cc_final: 0.8507 (p0) REVERT: F 606 THR cc_start: 0.8794 (m) cc_final: 0.8437 (p) REVERT: F 607 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8925 (mm-30) REVERT: F 630 ASP cc_start: 0.8812 (t0) cc_final: 0.8499 (t0) REVERT: I 332 MET cc_start: 0.3454 (mmp) cc_final: 0.3157 (mmm) REVERT: J 300 ILE cc_start: 0.7342 (mm) cc_final: 0.7042 (tp) outliers start: 1 outliers final: 0 residues processed: 531 average time/residue: 0.2236 time to fit residues: 192.4748 Evaluate side-chains 424 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 114 optimal weight: 0.0670 chunk 370 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 409 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 397 optimal weight: 50.0000 chunk 136 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 411 optimal weight: 0.0470 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 HIS ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.103302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.077646 restraints weight = 127539.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.079577 restraints weight = 84712.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.080847 restraints weight = 62989.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081552 restraints weight = 50776.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.082244 restraints weight = 43570.690| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33789 Z= 0.124 Angle : 0.691 10.772 45698 Z= 0.350 Chirality : 0.047 0.232 5167 Planarity : 0.005 0.072 5980 Dihedral : 7.825 119.183 4666 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.49 % Favored : 91.48 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4157 helix: 0.30 (0.13), residues: 1660 sheet: -1.17 (0.22), residues: 521 loop : -2.12 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 711 TYR 0.018 0.001 TYR F 244 PHE 0.030 0.002 PHE B 506 TRP 0.033 0.002 TRP C 551 HIS 0.004 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (33789) covalent geometry : angle 0.69089 / 0.35 (45698) hydrogen bonds : bond 0.03073 / 2.03 ( 1175) hydrogen bonds : angle 5.04962 / 3.49 ( 3405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6502.04 seconds wall clock time: 113 minutes 5.08 seconds (6785.08 seconds total)