Starting phenix.real_space_refine on Mon Jul 6 00:31:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tes_25851/07_2026/7tes_25851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tes_25851/07_2026/7tes_25851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tes_25851/07_2026/7tes_25851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tes_25851/07_2026/7tes_25851.map" model { file = "/net/cci-nas-00/data/ceres_data/7tes_25851/07_2026/7tes_25851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tes_25851/07_2026/7tes_25851.cif" } resolution = 4.7 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= 0.044 sd= 0.408 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 184 5.16 5 C 19946 2.51 5 N 5244 2.21 5 O 5932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31306 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6225 Classifications: {'peptide': 789} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 755} Chain breaks: 6 Chain: "B" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6117 Classifications: {'peptide': 774} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 746} Chain breaks: 3 Chain: "H" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1633 Classifications: {'peptide': 215} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 199} Chain breaks: 1 Chain: "L" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1678 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Restraints were copied for chains: C, D, M, N Time building chain proxies: 10.35, per 1000 atoms: 0.33 Number of scatterers: 31306 At special positions: 0 Unit cell: (168.51, 228.79, 179.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 184 16.00 O 5932 8.00 N 5244 7.00 C 19946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.02 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.02 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.05 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.02 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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: 2.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7436 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 74 sheets defined 34.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.244A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.530A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.681A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.590A pdb=" N THR A 222 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 223 " --> pdb=" O PRO A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 223' Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.811A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.577A pdb=" N ARG A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.730A pdb=" N LEU A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.712A pdb=" N ASP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.878A pdb=" N ARG A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 removed outlier: 4.023A pdb=" N ASP A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 removed outlier: 3.527A pdb=" N LEU A 527 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 548 removed outlier: 3.523A pdb=" N ALA A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.557A pdb=" N SER A 574 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 575 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 602 Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.842A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 678 removed outlier: 3.995A pdb=" N VAL A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 689 removed outlier: 4.134A pdb=" N ASN A 689 " --> pdb=" O THR A 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 689' Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.634A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 removed outlier: 3.618A pdb=" N ARG A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS A 726 " --> pdb=" O THR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.904A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.504A pdb=" N GLN A 791 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 835 through 862 removed outlier: 3.615A pdb=" N VAL A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.517A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 removed outlier: 3.978A pdb=" N LEU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.902A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.747A pdb=" N TYR B 252 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 removed outlier: 3.673A pdb=" N ARG B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 removed outlier: 3.572A pdb=" N ARG B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 459 through 471 Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 555 through 569 removed outlier: 4.825A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 577 Processing helix chain 'B' and resid 601 through 611 Processing helix chain 'B' and resid 626 through 656 removed outlier: 3.579A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.989A pdb=" N ASP B 668 " --> pdb=" O GLY B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.877A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.660A pdb=" N HIS B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 785 removed outlier: 4.425A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.758A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 843 removed outlier: 3.870A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 831 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 72 through 82 removed outlier: 4.244A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.530A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 145 through 155 removed outlier: 3.682A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.590A pdb=" N THR C 222 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS C 223 " --> pdb=" O PRO C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 223' Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.812A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 removed outlier: 3.577A pdb=" N ARG C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.730A pdb=" N LEU C 280 " --> pdb=" O GLY C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.711A pdb=" N ASP C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 346 removed outlier: 3.877A pdb=" N ARG C 344 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 removed outlier: 4.023A pdb=" N ASP C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 527 removed outlier: 3.528A pdb=" N LEU C 527 " --> pdb=" O MET C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 548 removed outlier: 3.523A pdb=" N ALA C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 576 removed outlier: 3.558A pdb=" N SER C 574 " --> pdb=" O THR C 571 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 575 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 602 Processing helix chain 'C' and resid 624 through 629 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.843A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 678 removed outlier: 3.995A pdb=" N VAL C 677 " --> pdb=" O ALA C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 689 removed outlier: 4.134A pdb=" N ASN C 689 " --> pdb=" O THR C 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 686 through 689' Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.634A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 730 removed outlier: 3.618A pdb=" N ARG C 725 " --> pdb=" O SER C 721 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS C 726 " --> pdb=" O THR C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.903A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 787 through 791 removed outlier: 3.503A pdb=" N GLN C 791 " --> pdb=" O PRO C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 803 Processing helix chain 'C' and resid 804 through 813 Processing helix chain 'C' and resid 835 through 862 removed outlier: 3.615A pdb=" N VAL C 846 " --> pdb=" O ALA C 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 179 through 193 removed outlier: 3.517A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 removed outlier: 3.979A pdb=" N LEU D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.902A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.748A pdb=" N TYR D 252 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.673A pdb=" N ARG D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.572A pdb=" N ARG D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 459 through 471 Processing helix chain 'D' and resid 495 through 502 Processing helix chain 'D' and resid 503 through 505 No H-bonds generated for 'chain 'D' and resid 503 through 505' Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 555 through 569 removed outlier: 4.826A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL D 569 " --> pdb=" O MET D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 577 Processing helix chain 'D' and resid 601 through 611 Processing helix chain 'D' and resid 626 through 656 removed outlier: 3.579A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 669 removed outlier: 3.989A pdb=" N ASP D 668 " --> pdb=" O GLY D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.877A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.661A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 785 removed outlier: 4.425A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 796 removed outlier: 3.757A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 843 removed outlier: 3.871A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D 831 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 833 " --> pdb=" O MET D 829 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE D 834 " --> pdb=" O ALA D 830 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.595A pdb=" N THR L 130 " --> pdb=" O GLU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 191 removed outlier: 4.006A pdb=" N GLU L 191 " --> pdb=" O LYS L 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 187 through 191' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 126 through 131 removed outlier: 3.595A pdb=" N THR N 130 " --> pdb=" O GLU N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 191 removed outlier: 4.006A pdb=" N GLU N 191 " --> pdb=" O LYS N 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 187 through 191' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.432A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 291 removed outlier: 5.938A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 354 removed outlier: 4.138A pdb=" N ASP A 353 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 420 through 421 removed outlier: 3.510A pdb=" N ILE A 421 " --> pdb=" O GLU A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.503A pdb=" N LYS A 433 " --> pdb=" O CYS A 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 509 through 511 removed outlier: 4.099A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 534 through 535 Processing sheet with id=AB1, first strand: chain 'A' and resid 555 through 557 removed outlier: 3.657A pdb=" N LYS A 555 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB3, first strand: chain 'A' and resid 704 through 705 removed outlier: 6.507A pdb=" N THR A 704 " --> pdb=" O TYR A 732 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 68 removed outlier: 8.704A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.576A pdb=" N VAL B 42 " --> pdb=" O ALA B 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 124 through 125 removed outlier: 3.639A pdb=" N GLY B 125 " --> pdb=" O PHE B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.896A pdb=" N THR B 173 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 172 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 230 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 341 through 344 Processing sheet with id=AB9, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.078A pdb=" N MET B 508 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.538A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AC3, first strand: chain 'B' and resid 524 through 525 Processing sheet with id=AC4, first strand: chain 'B' and resid 530 through 532 removed outlier: 3.818A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 534 through 535 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AC7, first strand: chain 'B' and resid 683 through 684 Processing sheet with id=AC8, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AC9, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.432A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 164 through 167 Processing sheet with id=AD2, first strand: chain 'C' and resid 288 through 291 removed outlier: 5.937A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 351 through 354 removed outlier: 4.138A pdb=" N ASP C 353 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 420 through 421 removed outlier: 3.510A pdb=" N ILE C 421 " --> pdb=" O GLU C 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 431 through 433 removed outlier: 3.503A pdb=" N LYS C 433 " --> pdb=" O CYS C 475 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 509 through 511 removed outlier: 4.099A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 534 through 535 Processing sheet with id=AD8, first strand: chain 'C' and resid 555 through 557 removed outlier: 3.656A pdb=" N LYS C 555 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AE1, first strand: chain 'C' and resid 704 through 705 removed outlier: 6.507A pdb=" N THR C 704 " --> pdb=" O TYR C 732 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 66 through 68 removed outlier: 8.704A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.576A pdb=" N VAL D 42 " --> pdb=" O ALA D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 124 through 125 removed outlier: 3.639A pdb=" N GLY D 125 " --> pdb=" O PHE D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.896A pdb=" N THR D 173 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 172 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 341 through 344 Processing sheet with id=AE7, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.077A pdb=" N MET D 508 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER D 407 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 434 through 438 removed outlier: 3.538A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE D 453 " --> pdb=" O LYS D 438 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AF1, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AF2, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.817A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 534 through 535 Processing sheet with id=AF4, first strand: chain 'D' and resid 537 through 539 Processing sheet with id=AF5, first strand: chain 'D' and resid 683 through 684 Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.508A pdb=" N THR H 116 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.725A pdb=" N SER H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER H 186 " --> pdb=" O HIS H 170 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS H 170 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.725A pdb=" N SER H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN H 177 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL H 175 " --> pdb=" O THR H 182 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.634A pdb=" N VAL H 203 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL H 212 " --> pdb=" O VAL H 203 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.028A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR L 106 " --> pdb=" O TYR L 90 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR L 90 " --> pdb=" O THR L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'L' and resid 57 through 58 removed outlier: 5.199A pdb=" N LEU L 50 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN L 41 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS L 38 " --> pdb=" O GLN L 93 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 133 through 137 Processing sheet with id=AG7, first strand: chain 'L' and resid 140 through 143 removed outlier: 4.034A pdb=" N ASN L 142 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER L 178 " --> pdb=" O THR L 168 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 157 through 158 removed outlier: 3.949A pdb=" N ASN L 149 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR L 196 " --> pdb=" O PHE L 213 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE L 213 " --> pdb=" O TYR L 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS L 198 " --> pdb=" O LYS L 211 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS L 211 " --> pdb=" O CYS L 198 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AH1, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.509A pdb=" N THR M 116 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 126 through 130 removed outlier: 3.726A pdb=" N SER M 126 " --> pdb=" O LYS M 149 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER M 186 " --> pdb=" O HIS M 170 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS M 170 " --> pdb=" O SER M 186 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 126 through 130 removed outlier: 3.726A pdb=" N SER M 126 " --> pdb=" O LYS M 149 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN M 177 " --> pdb=" O LEU M 180 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL M 175 " --> pdb=" O THR M 182 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 157 through 160 removed outlier: 3.634A pdb=" N VAL M 203 " --> pdb=" O VAL M 212 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL M 212 " --> pdb=" O VAL M 203 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AH6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AH7, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.027A pdb=" N LEU N 11 " --> pdb=" O GLU N 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR N 106 " --> pdb=" O TYR N 90 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR N 90 " --> pdb=" O THR N 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'N' and resid 57 through 58 removed outlier: 5.200A pdb=" N LEU N 50 " --> pdb=" O GLN N 41 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN N 41 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS N 38 " --> pdb=" O GLN N 93 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 133 through 137 Processing sheet with id=AI1, first strand: chain 'N' and resid 140 through 143 removed outlier: 4.034A pdb=" N ASN N 142 " --> pdb=" O TYR N 177 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR N 177 " --> pdb=" O ASN N 142 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER N 178 " --> pdb=" O THR N 168 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 157 through 158 removed outlier: 3.949A pdb=" N ASN N 149 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR N 196 " --> pdb=" O PHE N 213 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE N 213 " --> pdb=" O TYR N 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS N 198 " --> pdb=" O LYS N 211 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS N 211 " --> pdb=" O CYS N 198 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3072 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.15 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10002 1.34 - 1.46: 7173 1.46 - 1.58: 14511 1.58 - 1.70: 4 1.70 - 1.82: 308 Bond restraints: 31998 Sorted by residual: bond pdb=" CB LYS N 173 " pdb=" CG LYS N 173 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.67e+00 bond pdb=" CB LYS L 173 " pdb=" CG LYS L 173 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.56e+00 bond pdb=" CG LYS L 173 " pdb=" CD LYS L 173 " ideal model delta sigma weight residual 1.520 1.589 -0.069 3.00e-02 1.11e+03 5.35e+00 bond pdb=" CG LYS N 173 " pdb=" CD LYS N 173 " ideal model delta sigma weight residual 1.520 1.589 -0.069 3.00e-02 1.11e+03 5.26e+00 bond pdb=" C GLN C 577 " pdb=" N PRO C 578 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.20e+00 ... (remaining 31993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 43106 4.06 - 8.11: 222 8.11 - 12.17: 27 12.17 - 16.23: 7 16.23 - 20.29: 2 Bond angle restraints: 43364 Sorted by residual: angle pdb=" CB LYS L 173 " pdb=" CG LYS L 173 " pdb=" CD LYS L 173 " ideal model delta sigma weight residual 111.30 131.59 -20.29 2.30e+00 1.89e-01 7.78e+01 angle pdb=" CB LYS N 173 " pdb=" CG LYS N 173 " pdb=" CD LYS N 173 " ideal model delta sigma weight residual 111.30 131.58 -20.28 2.30e+00 1.89e-01 7.77e+01 angle pdb=" C PHE D 671 " pdb=" N GLN D 672 " pdb=" CA GLN D 672 " ideal model delta sigma weight residual 126.86 136.69 -9.83 1.57e+00 4.06e-01 3.92e+01 angle pdb=" C PHE B 671 " pdb=" N GLN B 672 " pdb=" CA GLN B 672 " ideal model delta sigma weight residual 126.86 136.67 -9.81 1.57e+00 4.06e-01 3.91e+01 angle pdb=" C THR M 138 " pdb=" N ASN M 139 " pdb=" CA ASN M 139 " ideal model delta sigma weight residual 121.70 132.71 -11.01 1.80e+00 3.09e-01 3.74e+01 ... (remaining 43359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 16965 17.45 - 34.90: 1779 34.90 - 52.35: 276 52.35 - 69.80: 108 69.80 - 87.25: 18 Dihedral angle restraints: 19146 sinusoidal: 7594 harmonic: 11552 Sorted by residual: dihedral pdb=" CA LYS D 670 " pdb=" C LYS D 670 " pdb=" N PHE D 671 " pdb=" CA PHE D 671 " ideal model delta harmonic sigma weight residual 180.00 -105.59 -74.41 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" CA LYS B 670 " pdb=" C LYS B 670 " pdb=" N PHE B 671 " pdb=" CA PHE B 671 " ideal model delta harmonic sigma weight residual -180.00 -105.61 -74.39 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N GLU B 200 " pdb=" CA GLU B 200 " ideal model delta harmonic sigma weight residual 180.00 112.23 67.77 0 5.00e+00 4.00e-02 1.84e+02 ... (remaining 19143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3677 0.057 - 0.113: 954 0.113 - 0.170: 190 0.170 - 0.226: 35 0.226 - 0.283: 2 Chirality restraints: 4858 Sorted by residual: chirality pdb=" CB ILE B 314 " pdb=" CA ILE B 314 " pdb=" CG1 ILE B 314 " pdb=" CG2 ILE B 314 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE D 314 " pdb=" CA ILE D 314 " pdb=" CG1 ILE D 314 " pdb=" CG2 ILE D 314 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA VAL M 187 " pdb=" N VAL M 187 " pdb=" C VAL M 187 " pdb=" CB VAL M 187 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4855 not shown) Planarity restraints: 5514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 577 " -0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO C 578 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 578 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 578 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 577 " 0.059 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO A 578 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 578 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 578 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 578 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C PRO A 578 " 0.050 2.00e-02 2.50e+03 pdb=" O PRO A 578 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 579 " -0.017 2.00e-02 2.50e+03 ... (remaining 5511 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7776 2.79 - 3.32: 29041 3.32 - 3.84: 55113 3.84 - 4.37: 62125 4.37 - 4.90: 100891 Nonbonded interactions: 254946 Sorted by model distance: nonbonded pdb=" O ILE B 133 " pdb=" OH TYR B 356 " model vdw 2.261 3.040 nonbonded pdb=" O ILE D 133 " pdb=" OH TYR D 356 " model vdw 2.261 3.040 nonbonded pdb=" O LEU D 465 " pdb=" OH TYR D 476 " model vdw 2.265 3.040 nonbonded pdb=" O LEU B 465 " pdb=" OH TYR B 476 " model vdw 2.266 3.040 nonbonded pdb=" OG SER D 469 " pdb=" OH TYR D 476 " model vdw 2.284 3.040 ... (remaining 254941 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'L' selection = chain 'N' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 31.740 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32014 Z= 0.202 Angle : 0.924 20.286 43396 Z= 0.510 Chirality : 0.053 0.283 4858 Planarity : 0.007 0.091 5514 Dihedral : 14.893 87.247 11662 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.85 % Favored : 90.89 % Rotamer: Outliers : 1.27 % Allowed : 8.11 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 2.38 % Twisted General : 0.63 % 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: -4.01 (0.11), residues: 3930 helix: -2.66 (0.10), residues: 1220 sheet: -2.47 (0.18), residues: 644 loop : -2.73 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 99 TYR 0.026 0.002 TYR C 724 PHE 0.019 0.002 PHE C 479 TRP 0.032 0.002 TRP B 610 HIS 0.005 0.002 HIS C 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (31998) covalent geometry : angle 0.92330 / 0.51 (43364) SS BOND : bond 0.00984 / 0.44 ( 16) SS BOND : angle 1.61554 / 1.06 ( 32) hydrogen bonds : bond 0.19577 / 13.37 ( 1098) hydrogen bonds : angle 8.28498 / 5.86 ( 3072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8748 (mmm) cc_final: 0.8405 (mmm) REVERT: A 576 MET cc_start: 0.8299 (mtm) cc_final: 0.8020 (mmm) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.0657 time to fit residues: 4.0587 Evaluate side-chains 32 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.243 Evaluate side-chains 55 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7484 (mtt) cc_final: 0.7157 (tpt) REVERT: B 387 LYS cc_start: 0.7972 (tptp) cc_final: 0.7242 (pttm) REVERT: B 388 TYR cc_start: 0.8801 (m-80) cc_final: 0.8133 (m-10) REVERT: B 465 LEU cc_start: 0.9367 (tp) cc_final: 0.9118 (tp) REVERT: B 562 MET cc_start: 0.9538 (ptp) cc_final: 0.9182 (ptp) REVERT: B 633 SER cc_start: 0.9534 (m) cc_final: 0.8387 (p) REVERT: B 829 MET cc_start: 0.9544 (mtp) cc_final: 0.9314 (tmm) outliers start: 7 outliers final: 0 residues processed: 54 average time/residue: 0.0655 time to fit residues: 5.0369 Evaluate side-chains 40 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.242 Evaluate side-chains 9 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 5 time to evaluate : 0.065 Fit side-chains REVERT: H 34 MET cc_start: 0.7904 (mpp) cc_final: 0.7575 (mpp) REVERT: H 83 MET cc_start: 0.8842 (mtm) cc_final: 0.8429 (mpp) outliers start: 4 outliers final: 1 residues processed: 9 average time/residue: 0.0351 time to fit residues: 0.4720 Evaluate side-chains 5 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.046 Evaluate side-chains 9 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 3 time to evaluate : 0.048 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 9 average time/residue: 0.0366 time to fit residues: 0.4672 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 2 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 0.0020 chunk 183 optimal weight: 2.9990 overall best weight: 2.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 171 HIS A 291 GLN A 389 ASN A 425 HIS ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 218 ASN H 77 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 HIS L 57 ASN L 94 HIS L 149 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.024075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.019488 restraints weight = 127625.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.020018 restraints weight = 84689.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.020408 restraints weight = 62476.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.020693 restraints weight = 49605.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.020896 restraints weight = 41560.711| |-----------------------------------------------------------------------------| r_work (final): 0.2542 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.027995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.022883 restraints weight = 118762.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.023420 restraints weight = 80978.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.023811 restraints weight = 61345.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.024097 restraints weight = 50227.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.024311 restraints weight = 42925.146| |-----------------------------------------------------------------------------| r_work (final): 0.2669 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.039430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.3238 r_free = 0.3238 target = 0.030761 restraints weight = 33277.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.029987 restraints weight = 53371.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.029915 restraints weight = 73232.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.029904 restraints weight = 88517.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.029904 restraints weight = 94987.723| |-----------------------------------------------------------------------------| r_work (final): 0.3107 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.037041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.025670 restraints weight = 39282.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.025676 restraints weight = 39312.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.025676 restraints weight = 39235.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.025676 restraints weight = 39235.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.025676 restraints weight = 39235.576| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32014 Z= 0.142 Angle : 0.692 10.458 43396 Z= 0.367 Chirality : 0.045 0.167 4858 Planarity : 0.005 0.079 5514 Dihedral : 7.327 70.678 4282 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.58 % Favored : 92.26 % Rotamer: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.12), residues: 3930 helix: -1.47 (0.12), residues: 1276 sheet: -2.40 (0.17), residues: 674 loop : -2.40 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 692 TYR 0.019 0.001 TYR C 724 PHE 0.034 0.001 PHE C 660 TRP 0.073 0.002 TRP D 610 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (31998) covalent geometry : angle 0.69081 / 0.37 (43364) SS BOND : bond 0.00586 / 0.32 ( 16) SS BOND : angle 1.72992 / 1.12 ( 32) hydrogen bonds : bond 0.04558 / 3.09 ( 1098) hydrogen bonds : angle 6.52403 / 4.63 ( 3072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.9261 (mmm) cc_final: 0.8809 (mmm) REVERT: A 375 MET cc_start: 0.7807 (mpp) cc_final: 0.7372 (mpp) REVERT: A 522 MET cc_start: 0.9294 (mpp) cc_final: 0.8799 (mpp) REVERT: A 523 MET cc_start: 0.9389 (mpp) cc_final: 0.9018 (mpp) REVERT: A 839 MET cc_start: 0.8190 (ptt) cc_final: 0.7869 (ppp) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0548 time to fit residues: 2.5988 Evaluate side-chains 27 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.234 Evaluate side-chains 40 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: D 142 MET cc_start: 0.8925 (mtt) cc_final: 0.8149 (tpp) REVERT: D 307 MET cc_start: 0.9592 (tmm) cc_final: 0.9131 (ppp) REVERT: D 388 TYR cc_start: 0.9080 (m-80) cc_final: 0.8769 (m-80) REVERT: D 508 MET cc_start: 0.9413 (mpp) cc_final: 0.8847 (mpp) REVERT: D 654 MET cc_start: 0.8348 (ptt) cc_final: 0.8042 (ptm) REVERT: D 706 MET cc_start: 0.9133 (tpt) cc_final: 0.8706 (tpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0728 time to fit residues: 4.1027 Evaluate side-chains 32 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.175 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.053 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 5 average time/residue: 0.0368 time to fit residues: 0.2891 Evaluate side-chains 4 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.064 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.065 Fit side-chains REVERT: N 179 MET cc_start: 0.2371 (tmm) cc_final: 0.2083 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0297 time to fit residues: 0.2022 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 207 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 285 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 chunk 231 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 340 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 274 optimal weight: 0.4980 chunk 271 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS D 159 ASN D 218 ASN D 782 GLN M 77 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 HIS N 57 ASN N 94 HIS N 128 GLN N 149 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.024726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.020072 restraints weight = 126190.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.020636 restraints weight = 81979.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.021047 restraints weight = 59783.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.021339 restraints weight = 47168.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.021560 restraints weight = 39241.848| |-----------------------------------------------------------------------------| r_work (final): 0.2567 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.027827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.022817 restraints weight = 117145.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.023403 restraints weight = 79132.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.023814 restraints weight = 59252.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.024109 restraints weight = 47712.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.024329 restraints weight = 40520.388| |-----------------------------------------------------------------------------| r_work (final): 0.2787 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.039777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 149)---------------| | r_work = 0.3236 r_free = 0.3236 target = 0.031394 restraints weight = 33157.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.031376 restraints weight = 68021.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.031319 restraints weight = 73884.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.031319 restraints weight = 87420.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.031319 restraints weight = 86901.248| |-----------------------------------------------------------------------------| r_work (final): 0.3227 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.036877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.025617 restraints weight = 40711.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.025617 restraints weight = 39997.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.025617 restraints weight = 39992.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.025617 restraints weight = 39983.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.025617 restraints weight = 39983.646| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32014 Z= 0.112 Angle : 0.640 9.570 43396 Z= 0.334 Chirality : 0.045 0.162 4858 Planarity : 0.005 0.074 5514 Dihedral : 6.801 57.400 4282 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.18 % Favored : 92.67 % Rotamer: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.12), residues: 3930 helix: -0.92 (0.13), residues: 1278 sheet: -2.21 (0.18), residues: 692 loop : -2.26 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 692 TYR 0.013 0.001 TYR C 372 PHE 0.025 0.001 PHE A 660 TRP 0.040 0.001 TRP B 610 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (31998) covalent geometry : angle 0.63914 / 0.33 (43364) SS BOND : bond 0.00365 / 0.18 ( 16) SS BOND : angle 1.58509 / 1.04 ( 32) hydrogen bonds : bond 0.04113 / 2.84 ( 1098) hydrogen bonds : angle 6.04437 / 4.29 ( 3072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.9197 (mmm) cc_final: 0.8734 (mmm) REVERT: A 522 MET cc_start: 0.9306 (mpp) cc_final: 0.9077 (mpp) REVERT: A 523 MET cc_start: 0.9394 (mpp) cc_final: 0.9057 (mtm) REVERT: A 783 MET cc_start: 0.6882 (ttt) cc_final: 0.6420 (ttt) REVERT: A 839 MET cc_start: 0.8141 (ptt) cc_final: 0.7803 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0508 time to fit residues: 2.3635 Evaluate side-chains 28 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.231 Evaluate side-chains 36 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: D 307 MET cc_start: 0.9530 (tmm) cc_final: 0.9095 (ppp) REVERT: D 388 TYR cc_start: 0.9216 (m-80) cc_final: 0.8950 (m-80) REVERT: D 642 PHE cc_start: 0.9562 (t80) cc_final: 0.9315 (t80) REVERT: D 654 MET cc_start: 0.8737 (ptt) cc_final: 0.8501 (ptm) REVERT: D 706 MET cc_start: 0.8958 (tpt) cc_final: 0.8746 (tpp) REVERT: D 824 MET cc_start: 0.7336 (mtm) cc_final: 0.6953 (mtm) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.0610 time to fit residues: 3.3052 Evaluate side-chains 32 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.179 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.051 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0337 time to fit residues: 0.2880 Evaluate side-chains 5 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.065 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.065 Fit side-chains REVERT: N 179 MET cc_start: 0.2499 (tmm) cc_final: 0.2207 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0349 time to fit residues: 0.2045 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 113 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 366 optimal weight: 40.0000 chunk 6 optimal weight: 0.0060 chunk 151 optimal weight: 0.0970 chunk 208 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 425 HIS A 726 HIS A 730 HIS D 649 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.024910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.020234 restraints weight = 123944.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.020802 restraints weight = 80771.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.021214 restraints weight = 59036.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.021506 restraints weight = 46685.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.021723 restraints weight = 38956.675| |-----------------------------------------------------------------------------| r_work (final): 0.2566 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.023925 restraints weight = 118984.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.024521 restraints weight = 80108.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.024944 restraints weight = 59972.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.025248 restraints weight = 48252.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.025474 restraints weight = 41076.052| |-----------------------------------------------------------------------------| r_work (final): 0.2713 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.039853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.033316 restraints weight = 37771.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.032499 restraints weight = 69802.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.032488 restraints weight = 103140.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.032484 restraints weight = 100612.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.032354 restraints weight = 104525.499| |-----------------------------------------------------------------------------| r_work (final): 0.3379 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.038493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.026407 restraints weight = 30875.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.026874 restraints weight = 23486.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.027247 restraints weight = 19831.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.027359 restraints weight = 17664.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.027360 restraints weight = 16597.523| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 32014 Z= 0.111 Angle : 0.634 11.910 43396 Z= 0.330 Chirality : 0.044 0.174 4858 Planarity : 0.004 0.071 5514 Dihedral : 6.501 56.688 4282 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.38 % Favored : 92.52 % Rotamer: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3930 helix: -0.60 (0.14), residues: 1282 sheet: -2.02 (0.18), residues: 712 loop : -2.21 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.015 0.001 TYR D 322 PHE 0.020 0.001 PHE A 838 TRP 0.079 0.002 TRP B 610 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (31998) covalent geometry : angle 0.63343 / 0.33 (43364) SS BOND : bond 0.00325 / 0.16 ( 16) SS BOND : angle 1.29681 / 0.86 ( 32) hydrogen bonds : bond 0.03951 / 2.72 ( 1098) hydrogen bonds : angle 5.88651 / 4.18 ( 3072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.239 Fit side-chains REVERT: A 261 MET cc_start: 0.9315 (mmm) cc_final: 0.8875 (mmm) REVERT: A 375 MET cc_start: 0.7655 (mpp) cc_final: 0.6842 (mpp) REVERT: A 522 MET cc_start: 0.9266 (mpp) cc_final: 0.9033 (mpp) REVERT: A 523 MET cc_start: 0.9392 (mpp) cc_final: 0.9036 (mtm) REVERT: A 576 MET cc_start: 0.8275 (mtm) cc_final: 0.8066 (mmm) REVERT: A 723 MET cc_start: 0.9045 (tpt) cc_final: 0.8836 (tpt) REVERT: A 839 MET cc_start: 0.8057 (ptt) cc_final: 0.7626 (ppp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0521 time to fit residues: 2.3695 Evaluate side-chains 27 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.219 Evaluate side-chains 35 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 134 MET cc_start: 0.8207 (mpp) cc_final: 0.7917 (tpp) REVERT: D 307 MET cc_start: 0.9626 (tmm) cc_final: 0.9211 (ppp) REVERT: D 388 TYR cc_start: 0.9226 (m-80) cc_final: 0.8948 (m-80) REVERT: D 562 MET cc_start: 0.9540 (ptp) cc_final: 0.9308 (ptp) REVERT: D 642 PHE cc_start: 0.9696 (t80) cc_final: 0.9398 (t80) REVERT: D 706 MET cc_start: 0.9167 (tpt) cc_final: 0.8896 (tpp) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.0570 time to fit residues: 3.0140 Evaluate side-chains 32 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.238 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.061 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0459 time to fit residues: 0.4051 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.063 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.063 Fit side-chains REVERT: N 179 MET cc_start: 0.1579 (tmm) cc_final: 0.1272 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0341 time to fit residues: 0.2219 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 372 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 266 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 298 optimal weight: 0.0670 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 ASN A 425 HIS ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.024780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.020111 restraints weight = 125210.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.020674 restraints weight = 81187.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.021076 restraints weight = 59296.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.021375 restraints weight = 46918.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.021592 restraints weight = 39036.674| |-----------------------------------------------------------------------------| r_work (final): 0.2562 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.028103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.023108 restraints weight = 118110.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.023699 restraints weight = 78760.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.024118 restraints weight = 58593.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.024417 restraints weight = 47116.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.024646 restraints weight = 39883.419| |-----------------------------------------------------------------------------| r_work (final): 0.2801 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.039996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.032812 restraints weight = 37209.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.032533 restraints weight = 51845.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.032530 restraints weight = 65263.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.032530 restraints weight = 65355.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.032530 restraints weight = 65355.853| |-----------------------------------------------------------------------------| r_work (final): 0.3162 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.037575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.026146 restraints weight = 40303.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.026146 restraints weight = 38901.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.026146 restraints weight = 38901.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.026146 restraints weight = 38901.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.026146 restraints weight = 38901.334| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32014 Z= 0.105 Angle : 0.634 10.720 43396 Z= 0.326 Chirality : 0.044 0.211 4858 Planarity : 0.004 0.068 5514 Dihedral : 6.355 56.210 4282 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.23 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.13), residues: 3930 helix: -0.33 (0.14), residues: 1278 sheet: -1.81 (0.18), residues: 694 loop : -2.14 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 327 TYR 0.012 0.001 TYR D 322 PHE 0.026 0.001 PHE C 660 TRP 0.048 0.001 TRP B 610 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (31998) covalent geometry : angle 0.63228 / 0.33 (43364) SS BOND : bond 0.00429 / 0.22 ( 16) SS BOND : angle 1.64703 / 1.07 ( 32) hydrogen bonds : bond 0.03833 / 2.66 ( 1098) hydrogen bonds : angle 5.73568 / 4.06 ( 3072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.266 Fit side-chains REVERT: C 261 MET cc_start: 0.9257 (mmm) cc_final: 0.8793 (mmm) REVERT: C 522 MET cc_start: 0.9302 (mpp) cc_final: 0.8905 (mpp) REVERT: C 523 MET cc_start: 0.9315 (mpp) cc_final: 0.9114 (mpp) REVERT: C 576 MET cc_start: 0.8407 (mtm) cc_final: 0.8135 (mmm) REVERT: C 839 MET cc_start: 0.8205 (ptt) cc_final: 0.7794 (ppp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0440 time to fit residues: 2.1104 Evaluate side-chains 29 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.229 Evaluate side-chains 35 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 388 TYR cc_start: 0.9198 (m-80) cc_final: 0.8926 (m-80) REVERT: D 637 PHE cc_start: 0.9396 (m-80) cc_final: 0.9049 (m-80) REVERT: D 642 PHE cc_start: 0.9552 (t80) cc_final: 0.9267 (t80) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0519 time to fit residues: 2.7201 Evaluate side-chains 32 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.232 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.037 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0476 time to fit residues: 0.3987 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.060 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.063 Fit side-chains REVERT: N 179 MET cc_start: 0.2137 (tmm) cc_final: 0.1885 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.2212 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 276 optimal weight: 0.0000 chunk 21 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 375 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 42 optimal weight: 0.3980 chunk 331 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 391 optimal weight: 40.0000 chunk 258 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 362 ASN C 425 HIS ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.024990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.020339 restraints weight = 123651.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.020911 restraints weight = 80874.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.021320 restraints weight = 59155.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.021616 restraints weight = 46736.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.021835 restraints weight = 38840.426| |-----------------------------------------------------------------------------| r_work (final): 0.2572 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.026837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.021392 restraints weight = 118554.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.021721 restraints weight = 91719.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.022148 restraints weight = 75958.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.022402 restraints weight = 64225.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.022589 restraints weight = 56627.618| |-----------------------------------------------------------------------------| r_work (final): 0.2685 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.042163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.032313 restraints weight = 29966.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.032804 restraints weight = 24075.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.033060 restraints weight = 20721.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.033279 restraints weight = 18931.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.033423 restraints weight = 17674.032| |-----------------------------------------------------------------------------| r_work (final): 0.3260 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.038025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.026531 restraints weight = 39614.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.026531 restraints weight = 38833.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.026531 restraints weight = 38834.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.026531 restraints weight = 38834.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.026531 restraints weight = 38834.056| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 32014 Z= 0.107 Angle : 0.626 13.431 43396 Z= 0.322 Chirality : 0.044 0.171 4858 Planarity : 0.004 0.066 5514 Dihedral : 6.165 55.240 4282 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.38 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.13), residues: 3930 helix: -0.26 (0.14), residues: 1302 sheet: -1.86 (0.18), residues: 698 loop : -2.11 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.012 0.001 TYR A 372 PHE 0.037 0.001 PHE C 660 TRP 0.044 0.001 TRP B 610 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (31998) covalent geometry : angle 0.62433 / 0.32 (43364) SS BOND : bond 0.00283 / 0.15 ( 16) SS BOND : angle 1.55193 / 1.02 ( 32) hydrogen bonds : bond 0.03746 / 2.59 ( 1098) hydrogen bonds : angle 5.62711 / 3.99 ( 3072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.9210 (mmm) cc_final: 0.8706 (mmm) REVERT: A 375 MET cc_start: 0.7481 (mpp) cc_final: 0.6680 (mpp) REVERT: A 522 MET cc_start: 0.9299 (mpp) cc_final: 0.9013 (mpp) REVERT: A 523 MET cc_start: 0.9326 (mpp) cc_final: 0.9102 (mtm) REVERT: A 723 MET cc_start: 0.9080 (tpt) cc_final: 0.8826 (tpt) REVERT: A 839 MET cc_start: 0.7733 (ptt) cc_final: 0.7414 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0512 time to fit residues: 2.3330 Evaluate side-chains 27 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.170 Evaluate side-chains 35 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 307 MET cc_start: 0.9434 (ppp) cc_final: 0.8871 (ppp) REVERT: D 388 TYR cc_start: 0.9304 (m-80) cc_final: 0.9010 (m-80) REVERT: D 637 PHE cc_start: 0.9471 (m-80) cc_final: 0.9164 (m-80) REVERT: D 642 PHE cc_start: 0.9665 (t80) cc_final: 0.9399 (t80) REVERT: D 706 MET cc_start: 0.9302 (tpt) cc_final: 0.8958 (tpt) REVERT: D 809 MET cc_start: 0.7002 (tpt) cc_final: 0.6547 (tpp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0586 time to fit residues: 3.1089 Evaluate side-chains 32 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.226 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.064 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0486 time to fit residues: 0.4259 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.061 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.065 Fit side-chains REVERT: N 179 MET cc_start: 0.2319 (tmm) cc_final: 0.2025 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.2221 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 385 optimal weight: 0.0870 chunk 146 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 364 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 84 optimal weight: 0.0020 chunk 216 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 388 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 ASN A 425 HIS A 791 GLN D 333 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.023938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.019378 restraints weight = 128192.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.019920 restraints weight = 84456.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.020308 restraints weight = 62238.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.020587 restraints weight = 49400.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.020791 restraints weight = 41364.111| |-----------------------------------------------------------------------------| r_work (final): 0.2533 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.026236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.020819 restraints weight = 121163.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.021289 restraints weight = 91323.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.021630 restraints weight = 73437.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.021883 restraints weight = 62163.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.022061 restraints weight = 54537.503| |-----------------------------------------------------------------------------| r_work (final): 0.2658 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.039403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.031458 restraints weight = 38011.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.031087 restraints weight = 52879.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.031078 restraints weight = 65433.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.031078 restraints weight = 65931.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.031078 restraints weight = 65931.701| |-----------------------------------------------------------------------------| r_work (final): 0.3103 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.038761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.026481 restraints weight = 30098.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.026901 restraints weight = 23761.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.027223 restraints weight = 20382.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.027327 restraints weight = 18453.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.027469 restraints weight = 17443.754| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32014 Z= 0.140 Angle : 0.637 12.829 43396 Z= 0.333 Chirality : 0.044 0.189 4858 Planarity : 0.004 0.066 5514 Dihedral : 6.124 55.454 4282 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.74 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.32 % 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: -1.99 (0.13), residues: 3930 helix: -0.04 (0.14), residues: 1294 sheet: -1.85 (0.18), residues: 734 loop : -2.00 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.012 0.001 TYR B 823 PHE 0.038 0.002 PHE A 660 TRP 0.040 0.002 TRP B 610 HIS 0.005 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (31998) covalent geometry : angle 0.63642 / 0.33 (43364) SS BOND : bond 0.00283 / 0.17 ( 16) SS BOND : angle 1.32863 / 0.87 ( 32) hydrogen bonds : bond 0.03649 / 2.51 ( 1098) hydrogen bonds : angle 5.60343 / 3.97 ( 3072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.9224 (mmm) cc_final: 0.8584 (mmt) REVERT: A 375 MET cc_start: 0.7719 (mpp) cc_final: 0.6874 (mpp) REVERT: A 522 MET cc_start: 0.9277 (mpp) cc_final: 0.9013 (mpp) REVERT: A 839 MET cc_start: 0.7872 (ptt) cc_final: 0.7572 (ppp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0619 time to fit residues: 2.7221 Evaluate side-chains 27 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.154 Evaluate side-chains 35 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 388 TYR cc_start: 0.9253 (m-80) cc_final: 0.8938 (m-80) REVERT: D 508 MET cc_start: 0.9461 (mpp) cc_final: 0.9027 (mpp) REVERT: D 637 PHE cc_start: 0.9481 (m-80) cc_final: 0.9176 (m-80) REVERT: D 706 MET cc_start: 0.9313 (tpt) cc_final: 0.9060 (tpp) REVERT: D 809 MET cc_start: 0.7143 (tpt) cc_final: 0.6272 (tpt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0566 time to fit residues: 3.0728 Evaluate side-chains 32 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.217 Evaluate side-chains 5 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.065 Fit side-chains REVERT: M 34 MET cc_start: 0.7275 (mpp) cc_final: 0.6753 (mpp) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0435 time to fit residues: 0.3295 Evaluate side-chains 5 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.061 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1447 time to fit residues: 0.6978 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 42 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 304 optimal weight: 9.9990 chunk 375 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 205 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 193 optimal weight: 0.3980 chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 312 optimal weight: 20.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.024166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.019628 restraints weight = 126766.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.020171 restraints weight = 83189.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.020555 restraints weight = 61133.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.020847 restraints weight = 48548.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.021051 restraints weight = 40580.987| |-----------------------------------------------------------------------------| r_work (final): 0.2545 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.026538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.020987 restraints weight = 122662.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.021305 restraints weight = 92610.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.021719 restraints weight = 77123.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.021988 restraints weight = 66098.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.022142 restraints weight = 57528.310| |-----------------------------------------------------------------------------| r_work (final): 0.2664 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.039810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.032364 restraints weight = 39166.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.032032 restraints weight = 52565.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.031991 restraints weight = 61919.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.031991 restraints weight = 64685.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.031991 restraints weight = 64685.734| |-----------------------------------------------------------------------------| r_work (final): 0.3133 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.038633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.026487 restraints weight = 29593.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.026920 restraints weight = 22871.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.027218 restraints weight = 19586.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.027322 restraints weight = 17634.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.027322 restraints weight = 16656.345| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32014 Z= 0.116 Angle : 0.637 13.770 43396 Z= 0.330 Chirality : 0.044 0.190 4858 Planarity : 0.004 0.065 5514 Dihedral : 6.095 55.227 4282 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.38 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.26 % 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: -1.94 (0.13), residues: 3930 helix: 0.01 (0.14), residues: 1292 sheet: -1.85 (0.18), residues: 734 loop : -1.97 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 192 TYR 0.028 0.001 TYR A 724 PHE 0.027 0.001 PHE A 660 TRP 0.090 0.002 TRP B 610 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (31998) covalent geometry : angle 0.63629 / 0.33 (43364) SS BOND : bond 0.00562 / 0.36 ( 16) SS BOND : angle 1.22756 / 0.77 ( 32) hydrogen bonds : bond 0.03667 / 2.56 ( 1098) hydrogen bonds : angle 5.60920 / 3.98 ( 3072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.9748 (ptp) cc_final: 0.9428 (mpp) REVERT: A 261 MET cc_start: 0.9195 (mmm) cc_final: 0.8775 (mmm) REVERT: A 375 MET cc_start: 0.7729 (mpp) cc_final: 0.6884 (mpp) REVERT: A 839 MET cc_start: 0.7863 (ptt) cc_final: 0.7561 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0592 time to fit residues: 2.7204 Evaluate side-chains 28 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.233 Evaluate side-chains 34 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 388 TYR cc_start: 0.9268 (m-80) cc_final: 0.8949 (m-80) REVERT: D 637 PHE cc_start: 0.9502 (m-80) cc_final: 0.9195 (m-80) REVERT: D 706 MET cc_start: 0.9337 (tpt) cc_final: 0.9039 (tpp) REVERT: D 809 MET cc_start: 0.7124 (tpt) cc_final: 0.6106 (tpt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0648 time to fit residues: 3.3642 Evaluate side-chains 32 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.158 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0377 time to fit residues: 0.3558 Evaluate side-chains 5 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.059 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0366 time to fit residues: 0.2320 Evaluate side-chains 2 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 315 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 257 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 302 optimal weight: 0.0170 chunk 166 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.024707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.020098 restraints weight = 125229.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.020663 restraints weight = 81839.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.021064 restraints weight = 59713.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.021355 restraints weight = 47215.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.021568 restraints weight = 39373.815| |-----------------------------------------------------------------------------| r_work (final): 0.2559 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.026913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.021424 restraints weight = 117611.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.021887 restraints weight = 89239.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.022162 restraints weight = 72074.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.022429 restraints weight = 62527.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.022589 restraints weight = 54940.586| |-----------------------------------------------------------------------------| r_work (final): 0.2681 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.039768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.033306 restraints weight = 38733.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.032375 restraints weight = 73434.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.031775 restraints weight = 108869.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.031446 restraints weight = 126793.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.031378 restraints weight = 145103.895| |-----------------------------------------------------------------------------| r_work (final): 0.3257 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.038782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.026576 restraints weight = 30682.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.027005 restraints weight = 23476.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.027386 restraints weight = 19977.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.027561 restraints weight = 17947.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.027697 restraints weight = 16781.847| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32014 Z= 0.104 Angle : 0.639 13.067 43396 Z= 0.326 Chirality : 0.044 0.180 4858 Planarity : 0.004 0.065 5514 Dihedral : 5.990 54.806 4282 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.12 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.26 % 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: -1.82 (0.13), residues: 3930 helix: 0.13 (0.15), residues: 1262 sheet: -1.73 (0.18), residues: 724 loop : -1.91 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 192 TYR 0.031 0.001 TYR A 724 PHE 0.024 0.001 PHE C 660 TRP 0.082 0.002 TRP B 610 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (31998) covalent geometry : angle 0.63807 / 0.33 (43364) SS BOND : bond 0.00205 / 0.12 ( 16) SS BOND : angle 1.20804 / 0.75 ( 32) hydrogen bonds : bond 0.03567 / 2.46 ( 1098) hydrogen bonds : angle 5.47576 / 3.88 ( 3072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.9186 (mmm) cc_final: 0.8752 (mmm) REVERT: A 375 MET cc_start: 0.7637 (mpp) cc_final: 0.6820 (mpp) REVERT: A 522 MET cc_start: 0.9356 (mpp) cc_final: 0.9131 (mpp) REVERT: A 655 MET cc_start: 0.8778 (mmp) cc_final: 0.8294 (mmm) REVERT: A 839 MET cc_start: 0.7869 (ptt) cc_final: 0.7577 (ppp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0610 time to fit residues: 2.8516 Evaluate side-chains 27 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.209 Evaluate side-chains 35 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 132 MET cc_start: 0.8838 (mmm) cc_final: 0.8519 (ppp) REVERT: D 388 TYR cc_start: 0.9295 (m-80) cc_final: 0.9004 (m-80) REVERT: D 637 PHE cc_start: 0.9507 (m-80) cc_final: 0.9176 (m-80) REVERT: D 809 MET cc_start: 0.6602 (tpt) cc_final: 0.5359 (tpt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0556 time to fit residues: 3.0194 Evaluate side-chains 32 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.202 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: M 83 MET cc_start: 0.7255 (mmp) cc_final: 0.6851 (mpp) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0389 time to fit residues: 0.3406 Evaluate side-chains 5 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.070 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0353 time to fit residues: 0.2245 Evaluate side-chains 2 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 244 optimal weight: 0.0010 chunk 193 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 384 optimal weight: 0.1980 chunk 331 optimal weight: 9.9990 chunk 192 optimal weight: 0.5980 chunk 288 optimal weight: 0.4980 chunk 111 optimal weight: 0.0070 chunk 271 optimal weight: 0.7980 chunk 246 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.025040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.020366 restraints weight = 125036.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.020948 restraints weight = 81550.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.021355 restraints weight = 59672.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.021653 restraints weight = 47069.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.021865 restraints weight = 39128.665| |-----------------------------------------------------------------------------| r_work (final): 0.2573 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.027121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.021487 restraints weight = 117823.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.021821 restraints weight = 91311.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.022245 restraints weight = 75669.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.022516 restraints weight = 64097.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.022719 restraints weight = 56316.803| |-----------------------------------------------------------------------------| r_work (final): 0.2688 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.042184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.032433 restraints weight = 29424.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.032963 restraints weight = 23368.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.033284 restraints weight = 19992.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.033388 restraints weight = 17972.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.033643 restraints weight = 16932.617| |-----------------------------------------------------------------------------| r_work (final): 0.3246 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.038973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.026833 restraints weight = 29485.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.027228 restraints weight = 23556.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.027527 restraints weight = 20456.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.027677 restraints weight = 18648.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.027677 restraints weight = 17458.559| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32014 Z= 0.105 Angle : 0.637 12.221 43396 Z= 0.325 Chirality : 0.044 0.183 4858 Planarity : 0.004 0.064 5514 Dihedral : 5.886 53.924 4282 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.26 % 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: -1.75 (0.13), residues: 3930 helix: 0.20 (0.15), residues: 1260 sheet: -1.70 (0.18), residues: 720 loop : -1.87 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 192 TYR 0.019 0.001 TYR C 724 PHE 0.037 0.001 PHE A 660 TRP 0.078 0.002 TRP B 610 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (31998) covalent geometry : angle 0.63609 / 0.32 (43364) SS BOND : bond 0.00412 / 0.16 ( 16) SS BOND : angle 1.46524 / 0.94 ( 32) hydrogen bonds : bond 0.03508 / 2.44 ( 1098) hydrogen bonds : angle 5.43246 / 3.84 ( 3072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7860 Ramachandran restraints generated. 3930 Oldfield, 0 Emsley, 3930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.9735 (ptp) cc_final: 0.9521 (ppp) REVERT: A 261 MET cc_start: 0.9131 (mmm) cc_final: 0.8538 (mmt) REVERT: A 375 MET cc_start: 0.7369 (mpp) cc_final: 0.6603 (mpp) REVERT: A 522 MET cc_start: 0.9363 (mpp) cc_final: 0.9093 (mpp) REVERT: A 655 MET cc_start: 0.8783 (mmp) cc_final: 0.8245 (mmm) REVERT: A 839 MET cc_start: 0.7916 (ptt) cc_final: 0.7592 (ppp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0608 time to fit residues: 2.6263 Evaluate side-chains 27 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.287 Evaluate side-chains 34 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 388 TYR cc_start: 0.9257 (m-80) cc_final: 0.8961 (m-80) REVERT: D 637 PHE cc_start: 0.9542 (m-80) cc_final: 0.9213 (m-80) REVERT: D 706 MET cc_start: 0.9364 (tpt) cc_final: 0.9009 (tpt) REVERT: D 809 MET cc_start: 0.6947 (tpt) cc_final: 0.5471 (tpt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0592 time to fit residues: 3.1093 Evaluate side-chains 33 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.181 Evaluate side-chains 6 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.063 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0483 time to fit residues: 0.4234 Evaluate side-chains 5 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.060 Evaluate side-chains 3 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0359 time to fit residues: 0.2434 Evaluate side-chains 2 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 203 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 281 optimal weight: 0.5980 chunk 336 optimal weight: 0.1980 chunk 264 optimal weight: 0.7980 chunk 347 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 239 optimal weight: 0.0370 chunk 184 optimal weight: 0.0030 chunk 286 optimal weight: 0.0970 overall best weight: 0.1866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.025283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.020581 restraints weight = 124286.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.021163 restraints weight = 81096.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.021569 restraints weight = 59366.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.021873 restraints weight = 46844.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.022094 restraints weight = 38884.777| |-----------------------------------------------------------------------------| r_work (final): 0.2580 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.027324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.021681 restraints weight = 117888.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.022147 restraints weight = 90246.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.022503 restraints weight = 73684.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.022818 restraints weight = 60063.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.022994 restraints weight = 53812.265| |-----------------------------------------------------------------------------| r_work (final): 0.2698 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.039733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.033753 restraints weight = 38379.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.032362 restraints weight = 67371.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.031932 restraints weight = 101691.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.031770 restraints weight = 107057.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.031720 restraints weight = 104045.030| |-----------------------------------------------------------------------------| r_work (final): 0.3466 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.038189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.026429 restraints weight = 39420.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.026429 restraints weight = 40327.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.026429 restraints weight = 40328.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.026429 restraints weight = 40328.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.026429 restraints weight = 40328.089| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32014 Z= 0.099 Angle : 0.625 12.064 43396 Z= 0.318 Chirality : 0.044 0.180 4858 Planarity : 0.004 0.064 5514 Dihedral : 5.777 53.190 4282 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.13), residues: 3930 helix: 0.33 (0.15), residues: 1262 sheet: -1.55 (0.18), residues: 688 loop : -1.84 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 469 TYR 0.023 0.001 TYR A 724 PHE 0.019 0.001 PHE A 660 TRP 0.071 0.002 TRP D 610 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (31998) covalent geometry : angle 0.62330 / 0.32 (43364) SS BOND : bond 0.00225 / 0.11 ( 16) SS BOND : angle 1.63195 / 1.06 ( 32) hydrogen bonds : bond 0.03417 / 2.35 ( 1098) hydrogen bonds : angle 5.31410 / 3.75 ( 3072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.52 seconds wall clock time: 51 minutes 53.14 seconds (3113.14 seconds total)