Starting phenix.real_space_refine on Thu May 29 01:54:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tes_25851/05_2025/7tes_25851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tes_25851/05_2025/7tes_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_25851/05_2025/7tes_25851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tes_25851/05_2025/7tes_25851.map" model { file = "/net/cci-nas-00/data/ceres_data/7tes_25851/05_2025/7tes_25851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tes_25851/05_2025/7tes_25851.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.044 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): 0.40s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, N, M Time building chain proxies: 28.05, per 1000 atoms: 0.90 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: 6.89 Conformation dependent library (CDL) restraints added in 3.9 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: 4.48 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: 12.12 Time building geometry restraints manager: 8.16 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'M' } 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 'L' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'M' } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 76.560 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 9.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.032 0.002 TRP B 610 HIS 0.005 0.002 HIS C 748 PHE 0.019 0.002 PHE C 479 TYR 0.026 0.002 TYR C 724 ARG 0.004 0.001 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.19577 ( 1098) hydrogen bonds : angle 8.28498 ( 3072) SS BOND : bond 0.00984 ( 16) SS BOND : angle 1.61554 ( 32) covalent geometry : bond 0.00394 (31998) covalent geometry : angle 0.92330 (43364) *********************** 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 : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8748 (mmm) cc_final: 0.8406 (mmm) REVERT: A 576 MET cc_start: 0.8299 (mtm) cc_final: 0.8019 (mmm) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.1711 time to fit residues: 10.3900 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 : 0.657 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 : 0.671 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: 0.1651 time to fit residues: 12.4341 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 : 0.622 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 : 0.175 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 9 average time/residue: 0.1105 time to fit residues: 1.3874 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 : 0.204 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 : 0.212 Fit side-chains REVERT: H 34 MET cc_start: 0.7905 (mpp) cc_final: 0.7576 (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: 0.0953 time to fit residues: 1.3088 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 : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 0.4980 chunk 298 optimal weight: 7.9990 chunk 165 optimal weight: 0.0270 chunk 102 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 159 optimal weight: 0.5980 chunk 308 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 187 optimal weight: 0.0870 chunk 229 optimal weight: 4.9990 chunk 357 optimal weight: 9.9990 overall best weight: 0.8418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 291 GLN A 389 ASN A 425 HIS Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 ASN D 218 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 HIS N 57 ASN N 94 HIS N 149 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.024646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.020051 restraints weight = 122980.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.020604 restraints weight = 81115.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.020997 restraints weight = 59602.373| |-----------------------------------------------------------------------------| r_work (final): 0.2535 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.028609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.023448 restraints weight = 116752.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.024017 restraints weight = 78846.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.024411 restraints weight = 59567.974| |-----------------------------------------------------------------------------| r_work (final): 0.2665 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.037162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.025857 restraints weight = 40463.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.025865 restraints weight = 39296.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.025865 restraints weight = 39066.594| |-----------------------------------------------------------------------------| r_work (final): 0.2930 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.039594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 139)---------------| | r_work = 0.3248 r_free = 0.3248 target = 0.031324 restraints weight = 33786.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.030935 restraints weight = 51799.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.030502 restraints weight = 79966.238| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32014 Z= 0.128 Angle : 0.688 10.532 43396 Z= 0.362 Chirality : 0.045 0.172 4858 Planarity : 0.005 0.078 5514 Dihedral : 7.274 70.508 4282 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.43 % Favored : 92.42 % Rotamer: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.12), residues: 3930 helix: -1.60 (0.12), residues: 1272 sheet: -2.38 (0.18), residues: 674 loop : -2.41 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 610 HIS 0.003 0.001 HIS A 146 PHE 0.035 0.001 PHE C 660 TYR 0.019 0.001 TYR C 724 ARG 0.005 0.000 ARG C 327 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 1098) hydrogen bonds : angle 6.48506 ( 3072) SS BOND : bond 0.00433 ( 16) SS BOND : angle 1.67162 ( 32) covalent geometry : bond 0.00269 (31998) covalent geometry : angle 0.68659 (43364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7852 Ramachandran restraints generated. 3926 Oldfield, 0 Emsley, 3926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7852 Ramachandran restraints generated. 3926 Oldfield, 0 Emsley, 3926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.9348 (mmm) cc_final: 0.8951 (mmm) REVERT: A 375 MET cc_start: 0.7893 (mpp) cc_final: 0.7505 (mpp) REVERT: A 522 MET cc_start: 0.9303 (mpp) cc_final: 0.9053 (mpp) REVERT: A 523 MET cc_start: 0.9376 (mpp) cc_final: 0.9059 (mtp) REVERT: A 783 MET cc_start: 0.7145 (ttt) cc_final: 0.6748 (ttt) REVERT: A 839 MET cc_start: 0.8186 (ptt) cc_final: 0.7879 (ppp) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.1643 time to fit residues: 8.1481 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 : 0.704 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 : 0.695 Fit side-chains revert: symmetry clash REVERT: D 142 MET cc_start: 0.8892 (mtt) cc_final: 0.8054 (tpt) REVERT: D 307 MET cc_start: 0.9600 (tmm) cc_final: 0.9134 (ppp) REVERT: D 388 TYR cc_start: 0.9217 (m-80) cc_final: 0.8894 (m-80) REVERT: D 508 MET cc_start: 0.9446 (mpp) cc_final: 0.8859 (mpp) REVERT: D 654 MET cc_start: 0.8339 (ptt) cc_final: 0.8031 (ptm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1790 time to fit residues: 10.1902 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 : 0.681 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 : 0.190 Fit side-chains REVERT: N 179 MET cc_start: 0.2675 (tmm) cc_final: 0.2436 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0948 time to fit residues: 0.6068 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 : 0.195 Evaluate side-chains 7 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.186 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 0.1192 time to fit residues: 1.0734 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 : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.5341 > 50: distance: 0 - 2: 7.965 distance: 3 - 4: 23.347 distance: 4 - 5: 35.108 distance: 4 - 7: 31.477 distance: 5 - 6: 22.809 distance: 5 - 11: 7.354 distance: 7 - 8: 51.890 distance: 8 - 9: 21.555 distance: 8 - 10: 31.597 distance: 11 - 12: 12.626 distance: 12 - 13: 41.950 distance: 12 - 15: 55.721 distance: 13 - 14: 54.449 distance: 13 - 22: 50.599 distance: 15 - 16: 47.104 distance: 16 - 17: 33.526 distance: 17 - 18: 20.692 distance: 18 - 19: 21.618 distance: 19 - 20: 6.236 distance: 19 - 21: 15.149 distance: 22 - 23: 43.192 distance: 22 - 28: 35.586 distance: 23 - 24: 36.272 distance: 23 - 26: 40.830 distance: 24 - 25: 24.140 distance: 24 - 29: 49.257 distance: 26 - 27: 35.208 distance: 27 - 28: 33.373 distance: 29 - 30: 10.060 distance: 30 - 31: 26.983 distance: 30 - 33: 46.445 distance: 31 - 32: 39.094 distance: 31 - 38: 27.859 distance: 33 - 34: 53.672 distance: 34 - 35: 32.489 distance: 35 - 36: 9.747 distance: 35 - 37: 16.439 distance: 38 - 39: 45.065 distance: 39 - 40: 23.910 distance: 39 - 42: 18.871 distance: 40 - 41: 36.085 distance: 40 - 47: 18.244 distance: 42 - 43: 40.313 distance: 43 - 44: 3.980 distance: 44 - 45: 28.767 distance: 44 - 46: 21.817 distance: 47 - 48: 23.237 distance: 48 - 49: 26.486 distance: 48 - 51: 15.616 distance: 49 - 50: 26.000 distance: 49 - 58: 30.723 distance: 51 - 52: 21.087 distance: 52 - 53: 22.616 distance: 53 - 54: 31.409 distance: 54 - 55: 35.782 distance: 55 - 56: 34.937 distance: 55 - 57: 26.447 distance: 58 - 59: 38.529 distance: 59 - 60: 53.274 distance: 59 - 62: 25.128 distance: 60 - 61: 32.917 distance: 60 - 66: 47.869 distance: 62 - 63: 41.854 distance: 62 - 64: 47.629 distance: 63 - 65: 37.815 distance: 66 - 67: 32.192 distance: 67 - 68: 36.742 distance: 67 - 70: 38.238 distance: 68 - 69: 39.084 distance: 68 - 73: 42.899 distance: 70 - 71: 58.382 distance: 70 - 72: 34.461 distance: 73 - 74: 24.541 distance: 74 - 75: 44.090 distance: 75 - 76: 39.754 distance: 75 - 77: 28.450 distance: 77 - 78: 34.486 distance: 78 - 79: 51.714 distance: 78 - 81: 4.758 distance: 79 - 80: 32.428 distance: 81 - 82: 38.794 distance: 81 - 83: 36.530 distance: 82 - 84: 27.925