Starting phenix.real_space_refine on Sat Feb 7 13:22:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9l_52963/02_2026/9q9l_52963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9l_52963/02_2026/9q9l_52963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q9l_52963/02_2026/9q9l_52963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9l_52963/02_2026/9q9l_52963.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9l_52963/02_2026/9q9l_52963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9l_52963/02_2026/9q9l_52963.cif" } resolution = 2.64 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 90 5.16 5 C 10464 2.51 5 N 2913 2.21 5 O 3069 1.98 5 H 16035 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32571 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 10857 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 662} Chain breaks: 1 Chain: "B" Number of atoms: 10857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 10857 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 662} Chain breaks: 1 Chain: "C" Number of atoms: 10857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 10857 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 662} Chain breaks: 1 Time building chain proxies: 5.89, per 1000 atoms: 0.18 Number of scatterers: 32571 At special positions: 0 Unit cell: (124.74, 116.82, 174.9, 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 90 16.00 O 3069 8.00 N 2913 7.00 C 10464 6.00 H 16035 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.06 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.05 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.06 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 532 " distance=2.05 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.05 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.05 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.05 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.05 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 392 " - pdb=" SG CYS B 532 " distance=2.05 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.05 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.06 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.05 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.05 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.06 Simple disulfide: pdb=" SG CYS C 392 " - pdb=" SG CYS C 532 " distance=2.05 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.05 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: 2.72 Conformation dependent library (CDL) restraints added in 864.0 milliseconds 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 33 sheets defined 37.7% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.584A pdb=" N GLU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.835A pdb=" N PHE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N HIS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.388A pdb=" N LEU A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 510 through 546 Proline residue: A 516 - end of helix removed outlier: 3.508A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 701 through 725 removed outlier: 3.593A pdb=" N LEU A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 4.196A pdb=" N MET A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 771 removed outlier: 4.448A pdb=" N VAL A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 804 Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 257 through 262 removed outlier: 4.321A pdb=" N PHE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.938A pdb=" N ASP B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.311A pdb=" N LEU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 removed outlier: 4.034A pdb=" N LEU B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 546 Proline residue: B 516 - end of helix removed outlier: 3.508A pdb=" N GLU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 701 through 725 Processing helix chain 'B' and resid 727 through 742 removed outlier: 4.202A pdb=" N MET B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 772 removed outlier: 4.584A pdb=" N VAL B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 755 " --> pdb=" O LYS B 751 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 770 " --> pdb=" O GLY B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 804 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 173 through 176 Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.949A pdb=" N MET C 183 " --> pdb=" O TYR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 250 through 254 removed outlier: 4.314A pdb=" N LYS C 253 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 256 No H-bonds generated for 'chain 'C' and resid 255 through 256' Processing helix chain 'C' and resid 257 through 265 removed outlier: 4.201A pdb=" N PHE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N HIS C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 429 Processing helix chain 'C' and resid 458 through 474 removed outlier: 4.384A pdb=" N LEU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 510 through 546 Proline residue: C 516 - end of helix removed outlier: 3.532A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 686 through 691 Processing helix chain 'C' and resid 701 through 725 removed outlier: 3.587A pdb=" N LEU C 714 " --> pdb=" O GLN C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 740 removed outlier: 4.108A pdb=" N MET C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 771 removed outlier: 4.304A pdb=" N VAL C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 755 " --> pdb=" O LYS C 751 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 771 " --> pdb=" O VAL C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 804 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.628A pdb=" N THR B 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.928A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP A 373 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY A 145 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET A 375 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR A 143 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG A 377 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN A 141 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 14.479A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.928A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP A 373 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY A 145 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET A 375 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR A 143 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG A 377 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN A 141 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 14.479A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.335A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA9, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.705A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 666 removed outlier: 6.676A pdb=" N THR A 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB5, first strand: chain 'B' and resid 559 through 563 removed outlier: 7.238A pdb=" N VAL B 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL C 667 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLN B 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 395 through 397 removed outlier: 5.631A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU B 374 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY B 145 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 376 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 143 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SER B 378 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN B 141 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 14.539A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 395 through 397 removed outlier: 5.631A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU B 374 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY B 145 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 376 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 143 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SER B 378 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN B 141 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 14.539A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 186 through 191 Processing sheet with id=AB9, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.308A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AC2, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC3, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'B' and resid 638 through 643 removed outlier: 6.710A pdb=" N TYR B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN B 658 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR B 649 " --> pdb=" O SER B 656 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AC7, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.874A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 14.522A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 395 through 397 removed outlier: 6.800A pdb=" N ARG C 377 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 142 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 14.522A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 185 through 191 Processing sheet with id=AD1, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.195A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AD3, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD4, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AD5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD6, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.772A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.19 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 16035 1.13 - 1.30: 2706 1.30 - 1.47: 7189 1.47 - 1.64: 6896 1.64 - 1.81: 144 Bond restraints: 32970 Sorted by residual: bond pdb=" NE2 HIS A 534 " pdb=" HE2 HIS A 534 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" NE2 HIS C 534 " pdb=" HE2 HIS C 534 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" NE2 HIS B 534 " pdb=" HE2 HIS B 534 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" NE2 GLN B 172 " pdb="HE22 GLN B 172 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" NE2 HIS C 681 " pdb=" HE2 HIS C 681 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 ... (remaining 32965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 42749 1.88 - 3.75: 12050 3.75 - 5.63: 2603 5.63 - 7.50: 1644 7.50 - 9.38: 165 Bond angle restraints: 59211 Sorted by residual: angle pdb=" CA ASP A 672 " pdb=" CB ASP A 672 " pdb=" CG ASP A 672 " ideal model delta sigma weight residual 112.60 120.15 -7.55 1.00e+00 1.00e+00 5.70e+01 angle pdb=" CA ASP C 672 " pdb=" CB ASP C 672 " pdb=" CG ASP C 672 " ideal model delta sigma weight residual 112.60 120.01 -7.41 1.00e+00 1.00e+00 5.49e+01 angle pdb=" CA ASP A 713 " pdb=" CB ASP A 713 " pdb=" CG ASP A 713 " ideal model delta sigma weight residual 112.60 119.45 -6.85 1.00e+00 1.00e+00 4.69e+01 angle pdb=" CA ASP B 672 " pdb=" CB ASP B 672 " pdb=" CG ASP B 672 " ideal model delta sigma weight residual 112.60 119.38 -6.78 1.00e+00 1.00e+00 4.60e+01 angle pdb=" CA ASP C 713 " pdb=" CB ASP C 713 " pdb=" CG ASP C 713 " ideal model delta sigma weight residual 112.60 119.36 -6.76 1.00e+00 1.00e+00 4.57e+01 ... (remaining 59206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 14432 17.68 - 35.37: 659 35.37 - 53.05: 254 53.05 - 70.73: 348 70.73 - 88.41: 12 Dihedral angle restraints: 15705 sinusoidal: 8367 harmonic: 7338 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual 93.00 171.67 -78.67 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual 93.00 169.54 -76.54 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 529 " pdb=" CB CYS A 529 " ideal model delta sinusoidal sigma weight residual 93.00 168.25 -75.25 1 1.00e+01 1.00e-02 7.16e+01 ... (remaining 15702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1665 0.109 - 0.218: 649 0.218 - 0.327: 140 0.327 - 0.436: 37 0.436 - 0.545: 11 Chirality restraints: 2502 Sorted by residual: chirality pdb=" CA ASP A 713 " pdb=" N ASP A 713 " pdb=" C ASP A 713 " pdb=" CB ASP A 713 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA ASP B 713 " pdb=" N ASP B 713 " pdb=" C ASP B 713 " pdb=" CB ASP B 713 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" CA ASP C 713 " pdb=" N ASP C 713 " pdb=" C ASP C 713 " pdb=" CB ASP C 713 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.91e+00 ... (remaining 2499 not shown) Planarity restraints: 4989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 369 " 0.198 2.00e-02 2.50e+03 7.10e-02 2.02e+02 pdb=" CG TRP B 369 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP B 369 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP B 369 " -0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP B 369 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TRP B 369 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 369 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 369 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 369 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP B 369 " 0.030 2.00e-02 2.50e+03 pdb=" HD1 TRP B 369 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP B 369 " -0.069 2.00e-02 2.50e+03 pdb=" HE3 TRP B 369 " -0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 369 " 0.091 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 369 " -0.057 2.00e-02 2.50e+03 pdb=" HH2 TRP B 369 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 174 " 0.136 2.00e-02 2.50e+03 6.94e-02 1.93e+02 pdb=" CG TRP C 174 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 174 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 174 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP C 174 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP C 174 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 174 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 174 " 0.055 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 174 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP C 174 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TRP C 174 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 TRP C 174 " -0.156 2.00e-02 2.50e+03 pdb=" HE3 TRP C 174 " -0.076 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 174 " 0.075 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 174 " -0.064 2.00e-02 2.50e+03 pdb=" HH2 TRP C 174 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 369 " 0.137 2.00e-02 2.50e+03 5.03e-02 1.01e+02 pdb=" CG TRP C 369 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 369 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP C 369 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP C 369 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP C 369 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 369 " -0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 369 " 0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 369 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP C 369 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 TRP C 369 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TRP C 369 " -0.050 2.00e-02 2.50e+03 pdb=" HE3 TRP C 369 " -0.044 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 369 " 0.074 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 369 " -0.049 2.00e-02 2.50e+03 pdb=" HH2 TRP C 369 " 0.037 2.00e-02 2.50e+03 ... (remaining 4986 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1088 2.13 - 2.75: 49178 2.75 - 3.37: 86951 3.37 - 3.98: 115924 3.98 - 4.60: 169943 Nonbonded interactions: 423084 Sorted by model distance: nonbonded pdb=" HG SER C 598 " pdb=" HG2 GLU C 631 " model vdw 1.516 2.270 nonbonded pdb=" HG SER B 598 " pdb=" HG2 GLU B 631 " model vdw 1.532 2.270 nonbonded pdb=" HG1 THR A 291 " pdb=" OD2 ASP A 293 " model vdw 1.602 2.450 nonbonded pdb=" HG1 THR C 291 " pdb=" OD2 ASP C 293 " model vdw 1.610 2.450 nonbonded pdb=" HG1 THR B 291 " pdb=" OD2 ASP B 293 " model vdw 1.610 2.450 ... (remaining 423079 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.680 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: 0.210 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.550 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.035 16953 Z= 0.543 Angle : 1.931 8.879 23022 Z= 1.303 Chirality : 0.123 0.545 2502 Planarity : 0.013 0.154 3006 Dihedral : 11.820 88.414 6150 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.14 % Allowed : 2.11 % Favored : 96.75 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2067 helix: -0.04 (0.18), residues: 633 sheet: -0.19 (0.24), residues: 402 loop : -0.63 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 627 TYR 0.113 0.014 TYR A 429 PHE 0.068 0.010 PHE B 683 TRP 0.123 0.022 TRP B 369 HIS 0.010 0.003 HIS C 248 Details of bonding type rmsd covalent geometry : bond 0.00943 (16935) covalent geometry : angle 1.93026 (22986) SS BOND : bond 0.02072 ( 18) SS BOND : angle 2.35117 ( 36) hydrogen bonds : bond 0.19824 ( 833) hydrogen bonds : angle 7.12294 ( 2535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 317 time to evaluate : 0.743 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: A 314 TYR cc_start: 0.7697 (m-80) cc_final: 0.7390 (m-80) REVERT: B 127 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: B 314 TYR cc_start: 0.7661 (m-80) cc_final: 0.7236 (m-80) REVERT: B 631 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: C 136 ARG cc_start: 0.7242 (mtm110) cc_final: 0.6958 (ptm160) REVERT: C 631 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7417 (pt0) outliers start: 20 outliers final: 1 residues processed: 334 average time/residue: 1.1136 time to fit residues: 416.4176 Evaluate side-chains 195 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 631 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS C 370 GLN C 445 ASN C 534 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.204840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144857 restraints weight = 48723.783| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.13 r_work: 0.3431 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16953 Z= 0.192 Angle : 0.619 4.957 23022 Z= 0.340 Chirality : 0.045 0.163 2502 Planarity : 0.005 0.043 3006 Dihedral : 5.222 74.192 2347 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.34 % Allowed : 9.70 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2067 helix: 1.19 (0.20), residues: 678 sheet: 0.34 (0.22), residues: 507 loop : -0.42 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 691 TYR 0.016 0.002 TYR B 653 PHE 0.018 0.002 PHE A 683 TRP 0.007 0.002 TRP A 174 HIS 0.009 0.001 HIS B 692 Details of bonding type rmsd covalent geometry : bond 0.00442 (16935) covalent geometry : angle 0.61377 (22986) SS BOND : bond 0.00834 ( 18) SS BOND : angle 2.06360 ( 36) hydrogen bonds : bond 0.05544 ( 833) hydrogen bonds : angle 5.16430 ( 2535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.994 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: A 131 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7911 (mtm180) REVERT: A 188 ASP cc_start: 0.5777 (t0) cc_final: 0.5442 (t70) REVERT: A 520 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7534 (ttt) REVERT: A 679 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: B 163 MET cc_start: 0.8177 (mtp) cc_final: 0.7967 (mtp) REVERT: B 349 LYS cc_start: 0.6723 (ttpt) cc_final: 0.6209 (mmtt) REVERT: B 421 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.5420 (mpp) REVERT: B 679 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: B 806 MET cc_start: 0.6879 (ppp) cc_final: 0.6338 (mtt) REVERT: C 349 LYS cc_start: 0.6898 (ttpt) cc_final: 0.6644 (ttmm) REVERT: C 371 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7948 (mt-10) REVERT: C 541 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7800 (tp30) outliers start: 41 outliers final: 11 residues processed: 255 average time/residue: 1.2730 time to fit residues: 363.8415 Evaluate side-chains 199 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 665 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 203 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 430 ASN B 248 HIS C 445 ASN C 620 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.191725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129182 restraints weight = 47064.632| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.04 r_work: 0.3230 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16953 Z= 0.149 Angle : 0.578 8.929 23022 Z= 0.315 Chirality : 0.043 0.273 2502 Planarity : 0.005 0.057 3006 Dihedral : 4.515 42.176 2339 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.40 % Allowed : 10.96 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.00 (0.18), residues: 2067 helix: 1.79 (0.21), residues: 675 sheet: 0.73 (0.22), residues: 507 loop : -0.20 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 136 TYR 0.013 0.001 TYR B 653 PHE 0.019 0.002 PHE C 287 TRP 0.011 0.002 TRP C 354 HIS 0.008 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00324 (16935) covalent geometry : angle 0.56593 (22986) SS BOND : bond 0.01222 ( 18) SS BOND : angle 3.04201 ( 36) hydrogen bonds : bond 0.04872 ( 833) hydrogen bonds : angle 4.65890 ( 2535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.878 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: A 541 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: A 679 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: B 349 LYS cc_start: 0.7457 (ttpt) cc_final: 0.7139 (tptt) REVERT: B 418 ARG cc_start: 0.7410 (mtp180) cc_final: 0.7197 (mtp180) REVERT: B 421 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.6354 (mpp) REVERT: B 607 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7098 (mp0) REVERT: C 223 PHE cc_start: 0.8372 (m-80) cc_final: 0.8136 (m-80) REVERT: C 511 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7220 (t0) REVERT: C 515 ARG cc_start: 0.7147 (tpp80) cc_final: 0.6725 (mpt180) REVERT: C 541 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: C 679 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7350 (tm-30) outliers start: 42 outliers final: 14 residues processed: 229 average time/residue: 1.1676 time to fit residues: 302.4274 Evaluate side-chains 192 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 511 ASN Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 679 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 80 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 430 ASN B 430 ASN B 692 HIS C 430 ASN C 445 ASN C 584 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119383 restraints weight = 46461.077| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.19 r_work: 0.3118 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16953 Z= 0.189 Angle : 0.594 11.084 23022 Z= 0.318 Chirality : 0.044 0.204 2502 Planarity : 0.005 0.052 3006 Dihedral : 4.819 39.356 2339 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.03 % Allowed : 12.10 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.15 (0.18), residues: 2067 helix: 1.95 (0.21), residues: 663 sheet: 0.97 (0.23), residues: 480 loop : -0.18 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 136 TYR 0.012 0.001 TYR A 314 PHE 0.022 0.002 PHE C 683 TRP 0.007 0.001 TRP A 354 HIS 0.008 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00451 (16935) covalent geometry : angle 0.57578 (22986) SS BOND : bond 0.01041 ( 18) SS BOND : angle 3.78237 ( 36) hydrogen bonds : bond 0.04584 ( 833) hydrogen bonds : angle 4.66748 ( 2535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.883 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: A 277 ASP cc_start: 0.8967 (m-30) cc_final: 0.8614 (m-30) REVERT: A 335 ARG cc_start: 0.7407 (ttp-170) cc_final: 0.6295 (tpp80) REVERT: A 515 ARG cc_start: 0.6852 (tpp80) cc_final: 0.6298 (mtt180) REVERT: A 679 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: B 188 ASP cc_start: 0.7022 (t0) cc_final: 0.6751 (t0) REVERT: B 277 ASP cc_start: 0.8951 (m-30) cc_final: 0.8614 (m-30) REVERT: B 349 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7706 (tptt) REVERT: B 421 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.6975 (mpp) REVERT: B 515 ARG cc_start: 0.6816 (tpp80) cc_final: 0.6400 (mpt-90) REVERT: C 509 THR cc_start: 0.7606 (p) cc_final: 0.7330 (p) REVERT: C 510 TYR cc_start: 0.8096 (m-80) cc_final: 0.7075 (m-80) REVERT: C 515 ARG cc_start: 0.6913 (tpp80) cc_final: 0.6579 (mtt180) REVERT: C 541 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7841 (tp30) REVERT: C 679 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7651 (tm-30) outliers start: 53 outliers final: 22 residues processed: 227 average time/residue: 1.2618 time to fit residues: 320.1932 Evaluate side-chains 211 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 679 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 32 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 620 ASN B 430 ASN C 248 HIS C 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117307 restraints weight = 46384.629| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.10 r_work: 0.3146 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16953 Z= 0.133 Angle : 0.517 7.034 23022 Z= 0.277 Chirality : 0.042 0.166 2502 Planarity : 0.004 0.048 3006 Dihedral : 4.549 36.101 2337 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.05 % Allowed : 13.70 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.31 (0.18), residues: 2067 helix: 2.20 (0.21), residues: 663 sheet: 0.96 (0.23), residues: 480 loop : -0.12 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 136 TYR 0.011 0.001 TYR B 653 PHE 0.018 0.001 PHE B 683 TRP 0.008 0.001 TRP A 354 HIS 0.006 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00308 (16935) covalent geometry : angle 0.50778 (22986) SS BOND : bond 0.00626 ( 18) SS BOND : angle 2.51329 ( 36) hydrogen bonds : bond 0.04076 ( 833) hydrogen bonds : angle 4.47706 ( 2535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.856 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: A 136 ARG cc_start: 0.7405 (ptm160) cc_final: 0.6921 (mtm110) REVERT: A 333 LYS cc_start: 0.8500 (mptp) cc_final: 0.8217 (mmtt) REVERT: A 335 ARG cc_start: 0.7350 (ttp-170) cc_final: 0.6109 (tpp80) REVERT: A 510 TYR cc_start: 0.7981 (m-10) cc_final: 0.7416 (m-80) REVERT: A 515 ARG cc_start: 0.6799 (tpp80) cc_final: 0.6272 (mtt180) REVERT: B 188 ASP cc_start: 0.7231 (t0) cc_final: 0.6859 (t0) REVERT: B 189 ARG cc_start: 0.7618 (ttm170) cc_final: 0.7283 (ttm170) REVERT: B 277 ASP cc_start: 0.8858 (m-30) cc_final: 0.8462 (m-30) REVERT: B 421 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7183 (mpp) REVERT: C 335 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.6215 (tpp80) REVERT: C 515 ARG cc_start: 0.7008 (tpp80) cc_final: 0.6582 (mtt180) REVERT: C 541 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: C 679 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7622 (tm-30) outliers start: 36 outliers final: 15 residues processed: 210 average time/residue: 1.3039 time to fit residues: 305.8245 Evaluate side-chains 202 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 175 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 0.0010 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 534 HIS A 620 ASN A 706 GLN B 430 ASN B 584 GLN C 430 ASN C 534 HIS C 620 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.179660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122050 restraints weight = 46285.443| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.29 r_work: 0.3013 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 16953 Z= 0.243 Angle : 0.624 10.185 23022 Z= 0.336 Chirality : 0.047 0.212 2502 Planarity : 0.006 0.078 3006 Dihedral : 5.096 40.471 2337 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.28 % Allowed : 13.41 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 1.10 (0.18), residues: 2067 helix: 2.00 (0.20), residues: 663 sheet: 0.93 (0.23), residues: 483 loop : -0.28 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 136 TYR 0.013 0.002 TYR C 296 PHE 0.022 0.002 PHE A 287 TRP 0.012 0.002 TRP A 354 HIS 0.010 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00592 (16935) covalent geometry : angle 0.61197 (22986) SS BOND : bond 0.00889 ( 18) SS BOND : angle 3.17457 ( 36) hydrogen bonds : bond 0.05016 ( 833) hydrogen bonds : angle 4.69905 ( 2535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.879 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: A 136 ARG cc_start: 0.7489 (ptm160) cc_final: 0.6932 (mtm110) REVERT: A 277 ASP cc_start: 0.8987 (m-30) cc_final: 0.8689 (m-30) REVERT: A 333 LYS cc_start: 0.8637 (mptp) cc_final: 0.8374 (mmtt) REVERT: A 421 MET cc_start: 0.8413 (mtt) cc_final: 0.7924 (tpp) REVERT: A 465 VAL cc_start: 0.8274 (t) cc_final: 0.8043 (m) REVERT: A 510 TYR cc_start: 0.7964 (m-10) cc_final: 0.7380 (m-80) REVERT: A 515 ARG cc_start: 0.7011 (tpp80) cc_final: 0.6759 (mpt180) REVERT: B 188 ASP cc_start: 0.7760 (t0) cc_final: 0.7373 (t0) REVERT: B 189 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7430 (ttm170) REVERT: B 212 LYS cc_start: 0.8289 (mptm) cc_final: 0.8043 (mptp) REVERT: B 277 ASP cc_start: 0.8989 (m-30) cc_final: 0.8677 (m-30) REVERT: B 421 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7089 (mpp) REVERT: C 189 ARG cc_start: 0.7323 (ttm170) cc_final: 0.7065 (ttm170) REVERT: C 366 MET cc_start: 0.8617 (mtt) cc_final: 0.8377 (mmt) REVERT: C 515 ARG cc_start: 0.7157 (tpp80) cc_final: 0.6726 (mtt180) REVERT: C 541 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: C 679 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7843 (tm-30) outliers start: 40 outliers final: 22 residues processed: 219 average time/residue: 1.3891 time to fit residues: 337.0375 Evaluate side-chains 209 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 679 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 40 optimal weight: 1.9990 chunk 182 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 ASN C 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125491 restraints weight = 46459.309| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.69 r_work: 0.3055 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16953 Z= 0.162 Angle : 0.539 8.084 23022 Z= 0.289 Chirality : 0.043 0.202 2502 Planarity : 0.004 0.046 3006 Dihedral : 4.801 39.752 2337 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.77 % Allowed : 14.67 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 1.24 (0.18), residues: 2067 helix: 2.22 (0.20), residues: 663 sheet: 0.90 (0.23), residues: 483 loop : -0.23 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 136 TYR 0.012 0.001 TYR A 301 PHE 0.017 0.001 PHE A 287 TRP 0.009 0.001 TRP A 354 HIS 0.005 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00387 (16935) covalent geometry : angle 0.52692 (22986) SS BOND : bond 0.00687 ( 18) SS BOND : angle 2.90650 ( 36) hydrogen bonds : bond 0.04215 ( 833) hydrogen bonds : angle 4.49155 ( 2535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.7392 (ptm160) cc_final: 0.6818 (mtm110) REVERT: A 333 LYS cc_start: 0.8621 (mptp) cc_final: 0.8374 (mmtt) REVERT: A 392 CYS cc_start: 0.4366 (OUTLIER) cc_final: 0.3411 (m) REVERT: A 421 MET cc_start: 0.8319 (mtt) cc_final: 0.7811 (tpp) REVERT: A 515 ARG cc_start: 0.6837 (tpp80) cc_final: 0.6574 (mpt180) REVERT: B 104 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6817 (tt) REVERT: B 188 ASP cc_start: 0.7707 (t0) cc_final: 0.7266 (t0) REVERT: B 189 ARG cc_start: 0.7658 (ttm170) cc_final: 0.7339 (ttm170) REVERT: B 212 LYS cc_start: 0.8305 (mptm) cc_final: 0.7929 (mptp) REVERT: B 277 ASP cc_start: 0.8966 (m-30) cc_final: 0.8596 (m-30) REVERT: B 421 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7117 (mpp) REVERT: B 515 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6518 (mpt180) REVERT: C 189 ARG cc_start: 0.7294 (ttm170) cc_final: 0.6969 (ttm170) REVERT: C 335 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.6077 (tpp80) REVERT: C 515 ARG cc_start: 0.6996 (tpp80) cc_final: 0.6579 (mtt180) REVERT: C 530 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7620 (mm-30) REVERT: C 679 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7668 (tm-30) outliers start: 31 outliers final: 15 residues processed: 201 average time/residue: 1.3181 time to fit residues: 294.2639 Evaluate side-chains 194 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 515 ARG Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 64 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 ASN C 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.180732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119605 restraints weight = 46360.650| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.89 r_work: 0.3106 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.7515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16953 Z= 0.155 Angle : 0.530 8.236 23022 Z= 0.284 Chirality : 0.043 0.178 2502 Planarity : 0.004 0.059 3006 Dihedral : 4.725 37.635 2337 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.66 % Allowed : 15.30 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 1.30 (0.19), residues: 2067 helix: 2.31 (0.20), residues: 663 sheet: 0.90 (0.23), residues: 483 loop : -0.20 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 136 TYR 0.015 0.001 TYR A 301 PHE 0.017 0.001 PHE A 287 TRP 0.009 0.001 TRP A 354 HIS 0.005 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00371 (16935) covalent geometry : angle 0.52151 (22986) SS BOND : bond 0.00636 ( 18) SS BOND : angle 2.44569 ( 36) hydrogen bonds : bond 0.04111 ( 833) hydrogen bonds : angle 4.45312 ( 2535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.7417 (ptm160) cc_final: 0.6906 (mtm110) REVERT: A 333 LYS cc_start: 0.8716 (mptp) cc_final: 0.8479 (mmtt) REVERT: A 421 MET cc_start: 0.8399 (mtt) cc_final: 0.7966 (tpp) REVERT: B 188 ASP cc_start: 0.7755 (t0) cc_final: 0.7336 (t0) REVERT: B 189 ARG cc_start: 0.7663 (ttm170) cc_final: 0.7352 (ttm170) REVERT: B 277 ASP cc_start: 0.8875 (m-30) cc_final: 0.8491 (m-30) REVERT: B 421 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: C 189 ARG cc_start: 0.7366 (ttm170) cc_final: 0.7149 (ttm170) REVERT: C 335 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.6258 (tpp80) REVERT: C 515 ARG cc_start: 0.7014 (tpp80) cc_final: 0.6554 (mtt180) REVERT: C 530 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7821 (mm-30) REVERT: C 679 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7702 (tm-30) outliers start: 29 outliers final: 18 residues processed: 196 average time/residue: 1.2384 time to fit residues: 269.8829 Evaluate side-chains 196 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 12 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 85 optimal weight: 0.0770 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS C 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121945 restraints weight = 46444.180| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.02 r_work: 0.3136 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.7595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16953 Z= 0.100 Angle : 0.483 8.256 23022 Z= 0.257 Chirality : 0.041 0.178 2502 Planarity : 0.004 0.062 3006 Dihedral : 4.425 35.831 2337 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.20 % Allowed : 15.87 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.49 (0.19), residues: 2067 helix: 2.53 (0.21), residues: 663 sheet: 0.92 (0.24), residues: 483 loop : -0.09 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 136 TYR 0.013 0.001 TYR A 301 PHE 0.014 0.001 PHE B 325 TRP 0.007 0.001 TRP A 354 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00225 (16935) covalent geometry : angle 0.47888 (22986) SS BOND : bond 0.00526 ( 18) SS BOND : angle 1.65687 ( 36) hydrogen bonds : bond 0.03426 ( 833) hydrogen bonds : angle 4.29167 ( 2535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.907 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: A 136 ARG cc_start: 0.7409 (ptm160) cc_final: 0.6934 (mtm110) REVERT: A 187 GLU cc_start: 0.7252 (pt0) cc_final: 0.6990 (mt-10) REVERT: A 333 LYS cc_start: 0.8723 (mptp) cc_final: 0.8500 (mmtt) REVERT: A 392 CYS cc_start: 0.2952 (OUTLIER) cc_final: 0.2725 (m) REVERT: A 421 MET cc_start: 0.8299 (mtt) cc_final: 0.8007 (tpp) REVERT: B 188 ASP cc_start: 0.7632 (t0) cc_final: 0.7184 (t0) REVERT: B 189 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7365 (ttm170) REVERT: B 277 ASP cc_start: 0.8782 (m-30) cc_final: 0.8418 (m-30) REVERT: B 421 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7385 (mpp) REVERT: B 607 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7000 (mp0) REVERT: C 335 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.6334 (tpp80) REVERT: C 421 MET cc_start: 0.8338 (mtt) cc_final: 0.7911 (tpp) REVERT: C 515 ARG cc_start: 0.6911 (tpp80) cc_final: 0.6533 (mtt180) REVERT: C 530 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7877 (mm-30) REVERT: C 679 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7539 (tm-30) outliers start: 21 outliers final: 11 residues processed: 194 average time/residue: 1.3223 time to fit residues: 285.4543 Evaluate side-chains 187 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 158 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 201 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.181631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119279 restraints weight = 46684.672| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.00 r_work: 0.3116 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.7642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16953 Z= 0.135 Angle : 0.514 7.960 23022 Z= 0.273 Chirality : 0.042 0.176 2502 Planarity : 0.004 0.068 3006 Dihedral : 4.518 36.773 2337 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.86 % Allowed : 16.27 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.48 (0.19), residues: 2067 helix: 2.51 (0.21), residues: 663 sheet: 0.94 (0.24), residues: 483 loop : -0.11 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 136 TYR 0.020 0.001 TYR C 301 PHE 0.016 0.001 PHE A 287 TRP 0.007 0.001 TRP A 354 HIS 0.004 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00319 (16935) covalent geometry : angle 0.50825 (22986) SS BOND : bond 0.00602 ( 18) SS BOND : angle 2.04556 ( 36) hydrogen bonds : bond 0.03782 ( 833) hydrogen bonds : angle 4.34584 ( 2535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.7368 (ptm160) cc_final: 0.6817 (mtm110) REVERT: A 187 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: A 333 LYS cc_start: 0.8660 (mptp) cc_final: 0.8424 (mmtt) REVERT: A 392 CYS cc_start: 0.3238 (OUTLIER) cc_final: 0.2844 (m) REVERT: A 421 MET cc_start: 0.8170 (mtt) cc_final: 0.7855 (tpp) REVERT: B 188 ASP cc_start: 0.7684 (t0) cc_final: 0.7188 (t0) REVERT: B 189 ARG cc_start: 0.7580 (ttm170) cc_final: 0.7235 (ttm170) REVERT: B 277 ASP cc_start: 0.8874 (m-30) cc_final: 0.8480 (m-30) REVERT: B 421 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7181 (mpp) REVERT: C 335 ARG cc_start: 0.7364 (ttp-170) cc_final: 0.6153 (tpp80) REVERT: C 421 MET cc_start: 0.8224 (mtt) cc_final: 0.7776 (tpp) REVERT: C 515 ARG cc_start: 0.6876 (tpp80) cc_final: 0.6393 (mtt180) REVERT: C 530 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7599 (mm-30) REVERT: C 679 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7511 (tm-30) outliers start: 15 outliers final: 10 residues processed: 186 average time/residue: 1.3889 time to fit residues: 287.1272 Evaluate side-chains 187 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 127 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS C 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.179494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117948 restraints weight = 47102.692| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.99 r_work: 0.3090 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.7778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16953 Z= 0.190 Angle : 0.564 9.000 23022 Z= 0.300 Chirality : 0.044 0.175 2502 Planarity : 0.005 0.067 3006 Dihedral : 4.775 40.052 2337 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.97 % Allowed : 16.27 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.34 (0.19), residues: 2067 helix: 2.38 (0.21), residues: 663 sheet: 0.91 (0.23), residues: 483 loop : -0.20 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 136 TYR 0.024 0.001 TYR C 301 PHE 0.019 0.002 PHE A 287 TRP 0.010 0.001 TRP B 354 HIS 0.006 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00460 (16935) covalent geometry : angle 0.55591 (22986) SS BOND : bond 0.00723 ( 18) SS BOND : angle 2.50454 ( 36) hydrogen bonds : bond 0.04315 ( 833) hydrogen bonds : angle 4.47526 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13627.46 seconds wall clock time: 230 minutes 41.46 seconds (13841.46 seconds total)