Starting phenix.real_space_refine on Thu Mar 21 22:37:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/03_2024/7tes_25851.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/03_2024/7tes_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/03_2024/7tes_25851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/03_2024/7tes_25851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/03_2024/7tes_25851.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/03_2024/7tes_25851.pdb" } 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 Residue "A GLU 549": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "L GLU 158": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "N GLU 158": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31306 Number of models: 1 Model: "" Number of chains: 8 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: "C" 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: "D" 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} Chain: "M" 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: "N" 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} Time building chain proxies: 15.86, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 11.99 Conformation dependent library (CDL) restraints added in 5.8 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: 2.98 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: 11.40 Time building geometry restraints manager: 12.96 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: 96.89 - 104.89: 578 104.89 - 112.89: 17189 112.89 - 120.88: 15162 120.88 - 128.88: 10173 128.88 - 136.88: 262 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 2.440 nonbonded pdb=" O ILE D 133 " pdb=" OH TYR D 356 " model vdw 2.261 2.440 nonbonded pdb=" O LEU D 465 " pdb=" OH TYR D 476 " model vdw 2.265 2.440 nonbonded pdb=" O LEU B 465 " pdb=" OH TYR B 476 " model vdw 2.266 2.440 nonbonded pdb=" OG SER D 469 " pdb=" OH TYR D 476 " model vdw 2.284 2.440 ... (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 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: 0.820 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: 5.660 Check model and map are aligned: 0.430 Set scattering table: 0.290 Process input model: 78.300 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.630 ------------------------------------------------------------------------------- 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 31998 Z= 0.261 Angle : 0.923 20.286 43364 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.803 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: 0.1864 time to fit residues: 11.3365 Evaluate side-chains 32 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.804 Evaluate side-chains 55 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.762 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: 0.1847 time to fit residues: 13.8697 Evaluate side-chains 40 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.786 Evaluate side-chains 9 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 5 time to evaluate : 0.214 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: 0.0861 time to fit residues: 1.1885 Evaluate side-chains 5 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 4 time to evaluate : 0.212 Evaluate side-chains 9 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 3 time to evaluate : 0.214 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 9 average time/residue: 0.1260 time to fit residues: 1.6019 Evaluate side-chains 4 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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: 20.0000 chunk 298 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 308 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 187 optimal weight: 0.0670 chunk 229 optimal weight: 7.9990 chunk 357 optimal weight: 4.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 40 GLN A 47 ASN A 171 HIS A 291 GLN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN A 425 HIS Total number of N/Q/H flips: 7 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 180 GLN D 192 ASN D 218 ASN ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS D 698 ASN Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN N 6 GLN N 57 ASN ** N 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 GLN N 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31998 Z= 0.173 Angle : 0.671 11.380 43364 Z= 0.355 Chirality : 0.044 0.166 4858 Planarity : 0.005 0.078 5514 Dihedral : 7.307 72.035 4282 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.74 % Favored : 92.11 % Rotamer: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.53 % 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: -3.12 (0.12), residues: 3930 helix: -1.40 (0.13), residues: 1258 sheet: -2.38 (0.18), residues: 662 loop : -2.40 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 610 HIS 0.004 0.001 HIS B 127 PHE 0.032 0.001 PHE C 660 TYR 0.019 0.001 TYR A 724 ARG 0.004 0.000 ARG M 72 *********************** 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 31 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8769 (mmm) cc_final: 0.8350 (mmm) REVERT: A 375 MET cc_start: 0.7264 (mpp) cc_final: 0.6856 (mpp) REVERT: A 576 MET cc_start: 0.8201 (mtm) cc_final: 0.7924 (mmm) REVERT: A 839 MET cc_start: 0.8558 (ptt) cc_final: 0.8055 (ppp) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.1716 time to fit residues: 8.1082 Evaluate side-chains 27 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.746 Evaluate side-chains 40 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: D 142 MET cc_start: 0.7765 (mtt) cc_final: 0.7208 (tpt) REVERT: D 307 MET cc_start: 0.9162 (tmm) cc_final: 0.8855 (ppp) REVERT: D 465 LEU cc_start: 0.9408 (tp) cc_final: 0.9136 (tp) REVERT: D 654 MET cc_start: 0.8333 (ptt) cc_final: 0.8022 (ptm) REVERT: D 706 MET cc_start: 0.8743 (tpt) cc_final: 0.8127 (tpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1809 time to fit residues: 10.4055 Evaluate side-chains 33 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.730 Evaluate side-chains 6 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 5 time to evaluate : 0.187 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 5 average time/residue: 0.1300 time to fit residues: 1.0341 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.203 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.206 Fit side-chains REVERT: N 179 MET cc_start: 0.1046 (tmm) cc_final: 0.0770 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1008 time to fit residues: 0.6693 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 297 optimal weight: 7.9990 chunk 243 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 chunk 358 optimal weight: 8.9990 chunk 387 optimal weight: 0.0370 chunk 319 optimal weight: 5.9990 chunk 355 optimal weight: 30.0000 chunk 122 optimal weight: 0.0070 chunk 287 optimal weight: 10.0000 overall best weight: 0.9676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 31998 Z= 0.410 Angle : 0.933 20.062 43364 Z= 0.493 Chirality : 0.056 0.460 4858 Planarity : 0.008 0.109 5514 Dihedral : 7.267 65.051 4282 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.70 % Favored : 91.09 % Rotamer: Outliers : 0.12 % Allowed : 2.31 % Favored : 97.58 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.37 % 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: -3.14 (0.12), residues: 3930 helix: -1.43 (0.13), residues: 1262 sheet: -2.37 (0.17), residues: 662 loop : -2.41 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.005 TRP B 610 HIS 0.039 0.004 HIS A 314 PHE 0.066 0.004 PHE A 838 TYR 0.198 0.004 TYR A 816 ARG 0.092 0.002 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 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 fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8869 (mmm) cc_final: 0.8351 (mmm) REVERT: A 576 MET cc_start: 0.8187 (mtm) cc_final: 0.7948 (mmm) REVERT: A 662 MET cc_start: 0.7167 (mtp) cc_final: 0.6954 (mtp) REVERT: A 839 MET cc_start: 0.8557 (ptt) cc_final: 0.8042 (ppp) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.1609 time to fit residues: 7.3445 Evaluate side-chains 27 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.826 Evaluate side-chains 34 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: D 142 MET cc_start: 0.7787 (mtt) cc_final: 0.7497 (tpp) REVERT: D 307 MET cc_start: 0.9165 (tmm) cc_final: 0.8865 (ppp) REVERT: D 465 LEU cc_start: 0.9391 (tp) cc_final: 0.9117 (tp) REVERT: D 654 MET cc_start: 0.8319 (ptt) cc_final: 0.7996 (ptm) REVERT: D 706 MET cc_start: 0.8690 (tpt) cc_final: 0.8099 (tpp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1627 time to fit residues: 8.4486 Evaluate side-chains 33 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.725 Evaluate side-chains 6 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.194 Fit side-chains REVERT: H 34 MET cc_start: 0.8329 (mpp) cc_final: 0.7970 (mpp) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1132 time to fit residues: 1.0600 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.246 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.194 Fit side-chains REVERT: N 179 MET cc_start: 0.1719 (tmm) cc_final: 0.1504 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0960 time to fit residues: 0.6459 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4106 > 50: distance: 0 - 29: 27.923 distance: 1 - 2: 5.008 distance: 2 - 3: 40.973 distance: 4 - 5: 39.363 distance: 5 - 6: 34.705 distance: 5 - 8: 35.862 distance: 6 - 11: 40.111 distance: 8 - 10: 56.662 distance: 11 - 12: 39.707 distance: 12 - 13: 41.456 distance: 13 - 17: 56.995 distance: 15 - 16: 69.984 distance: 17 - 18: 41.463 distance: 18 - 19: 8.212 distance: 18 - 21: 9.913 distance: 19 - 29: 56.821 distance: 21 - 22: 40.038 distance: 22 - 23: 55.437 distance: 22 - 24: 40.648 distance: 24 - 26: 26.902 distance: 25 - 27: 56.151 distance: 26 - 27: 11.517 distance: 27 - 28: 57.843 distance: 29 - 30: 31.547 distance: 30 - 31: 33.643 distance: 30 - 33: 12.759 distance: 31 - 32: 56.223 distance: 31 - 36: 38.755 distance: 33 - 34: 40.709 distance: 33 - 35: 41.480 distance: 36 - 37: 18.718 distance: 37 - 38: 46.814 distance: 37 - 40: 16.585 distance: 38 - 39: 56.746 distance: 38 - 41: 5.947 distance: 41 - 42: 32.174 distance: 43 - 44: 40.336 distance: 43 - 45: 33.207 distance: 45 - 46: 7.622 distance: 46 - 47: 39.188 distance: 47 - 56: 43.603 distance: 49 - 50: 52.690 distance: 50 - 51: 9.298 distance: 50 - 52: 53.900 distance: 51 - 53: 26.956 distance: 53 - 55: 39.779 distance: 56 - 57: 60.940 distance: 57 - 58: 32.019 distance: 57 - 60: 39.159 distance: 58 - 59: 44.260 distance: 58 - 68: 50.162 distance: 60 - 61: 5.730 distance: 61 - 62: 39.084 distance: 61 - 63: 34.755 distance: 62 - 64: 38.806 distance: 64 - 66: 51.572 distance: 68 - 69: 16.957 distance: 69 - 70: 6.832 distance: 69 - 72: 40.452 distance: 70 - 71: 23.728 distance: 73 - 74: 40.673 distance: 74 - 75: 9.344