Starting phenix.real_space_refine on Sun Aug 11 04:52:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/08_2024/7tes_25851.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/08_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_25851/08_2024/7tes_25851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/08_2024/7tes_25851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/08_2024/7tes_25851.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tes_25851/08_2024/7tes_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 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: 0.45s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 16.29, per 1000 atoms: 0.52 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: 12.17 Conformation dependent library (CDL) restraints added in 5.4 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: 4.25 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: 13.15 Time building geometry restraints manager: 13.31 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 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: 0.00 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: 0.840 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: 1.340 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 81.850 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.150 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.670 ------------------------------------------------------------------------------- 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 : 0.782 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: 0.1699 time to fit residues: 10.3180 Evaluate side-chains 32 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.709 Evaluate side-chains 55 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.655 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: 0.1816 time to fit residues: 13.5317 Evaluate side-chains 40 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.759 Evaluate side-chains 9 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 5 time to evaluate : 0.203 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: 0.0942 time to fit residues: 1.2834 Evaluate side-chains 5 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 4 time to evaluate : 0.205 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: 0.1187 time to fit residues: 1.5037 Evaluate side-chains 4 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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: M 77 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 31998 Z= 0.173 Angle : 0.687 10.532 43364 Z= 0.361 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 D 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 A 327 *********************** 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 fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8930 (mmm) cc_final: 0.8615 (mmm) REVERT: A 375 MET cc_start: 0.7263 (mpp) cc_final: 0.7000 (mpp) REVERT: A 839 MET cc_start: 0.8538 (ptt) cc_final: 0.8168 (ppp) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.1658 time to fit residues: 8.1472 Evaluate side-chains 29 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.711 Evaluate side-chains 40 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: D 142 MET cc_start: 0.7700 (mtt) cc_final: 0.7150 (tpt) REVERT: D 307 MET cc_start: 0.9157 (tmm) cc_final: 0.8820 (ppp) REVERT: D 465 LEU cc_start: 0.9508 (tp) cc_final: 0.9272 (tp) REVERT: D 654 MET cc_start: 0.8317 (ptt) cc_final: 0.7859 (ptm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1883 time to fit residues: 10.7160 Evaluate side-chains 34 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.754 Evaluate side-chains 7 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 6 time to evaluate : 0.203 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 0.1271 time to fit residues: 1.1620 Evaluate side-chains 5 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.205 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.222 Fit side-chains REVERT: N 179 MET cc_start: 0.1978 (tmm) cc_final: 0.1712 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1017 time to fit residues: 0.6815 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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: 1.9990 chunk 111 optimal weight: 0.0370 chunk 297 optimal weight: 8.9990 chunk 243 optimal weight: 0.0870 chunk 98 optimal weight: 20.0000 chunk 358 optimal weight: 40.0000 chunk 387 optimal weight: 10.0000 chunk 319 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 287 optimal weight: 0.0020 overall best weight: 0.8248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 334 ASN A 425 HIS ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 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: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 HIS 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 6 GLN ** 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: 0.7774 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31998 Z= 0.266 Angle : 0.905 21.313 43364 Z= 0.467 Chirality : 0.058 1.091 4858 Planarity : 0.008 0.135 5514 Dihedral : 7.221 59.753 4282 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.55 % Favored : 91.20 % Rotamer: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.02 % Cbeta Deviations : 0.00 % 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: -3.34 (0.12), residues: 3930 helix: -1.79 (0.12), residues: 1272 sheet: -2.30 (0.18), residues: 666 loop : -2.45 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP C 151 HIS 0.040 0.003 HIS C 314 PHE 0.058 0.003 PHE C 630 TYR 0.067 0.003 TYR A 88 ARG 0.081 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 37 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8622 (mmm) cc_final: 0.8383 (mmm) REVERT: A 375 MET cc_start: 0.7465 (mpp) cc_final: 0.7155 (mpp) REVERT: A 576 MET cc_start: 0.8420 (mtm) cc_final: 0.8081 (mmm) REVERT: A 605 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7972 (p) REVERT: A 839 MET cc_start: 0.8589 (ptt) cc_final: 0.8049 (ppp) outliers start: 6 outliers final: 2 residues processed: 35 average time/residue: 0.1526 time to fit residues: 8.3867 Evaluate side-chains 32 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.802 Evaluate side-chains 35 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 142 MET cc_start: 0.7743 (mtt) cc_final: 0.7186 (tpt) REVERT: D 307 MET cc_start: 0.9165 (tmm) cc_final: 0.8821 (ppp) REVERT: D 465 LEU cc_start: 0.9502 (tp) cc_final: 0.9267 (tp) REVERT: D 654 MET cc_start: 0.8410 (ptt) cc_final: 0.7992 (ptm) REVERT: D 824 MET cc_start: 0.7494 (mtm) cc_final: 0.7173 (mtm) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1550 time to fit residues: 8.2821 Evaluate side-chains 32 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.682 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1325 time to fit residues: 0.9409 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.239 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.246 Fit side-chains REVERT: N 179 MET cc_start: 0.1767 (tmm) cc_final: 0.1544 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1200 time to fit residues: 0.8123 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 354 optimal weight: 50.0000 chunk 269 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 171 optimal weight: 0.0060 chunk 240 optimal weight: 0.0470 chunk 359 optimal weight: 2.9990 chunk 380 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 340 optimal weight: 6.9990 chunk 102 optimal weight: 0.0170 overall best weight: 0.7334 ------------------------------------------------------------------------------- NQH flips ********* Analyzi------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31998 Z= 0.266 Angle : 0.905 21.304 43364 Z= 0.467 Chirality : 0.058 1.089 4858 Planarity : 0.008 0.135 5514 Dihedral : 7.221 59.753 4282 Min Nonbonded Distance : 0.748 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.55 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % 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: -3.34 (0.12), residues: 3930 helix: -1.79 (0.12), residues: 1272 sheet: -2.30 (0.18), residues: 666 loop : -2.45 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP C 151 HIS 0.040 0.003 HIS A 314 PHE 0.058 0.003 PHE A 630 TYR 0.067 0.003 TYR C 88 ARG 0.081 0.002 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 4 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 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8640 (mmm) cc_final: 0.8387 (mmm) REVERT: A 375 MET cc_start: 0.7460 (mpp) cc_final: 0.7153 (mpp) REVERT: A 576 MET cc_start: 0.8420 (mtm) cc_final: 0.8087 (mmm) REVERT: A 839 MET cc_start: 0.8588 (ptt) cc_final: 0.8052 (ppp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1458 time to fit residues: 6.4553 Evaluate side-chains 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.553 Evaluate side-chains 33 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 142 MET cc_start: 0.7743 (mtt) cc_final: 0.7184 (tpt) REVERT: D 307 MET cc_start: 0.9165 (tmm) cc_final: 0.8821 (ppp) REVERT: D 388 TYR cc_start: 0.8511 (m-80) cc_final: 0.8295 (m-80) REVERT: D 465 LEU cc_start: 0.9505 (tp) cc_final: 0.9270 (tp) REVERT: D 654 MET cc_start: 0.8405 (ptt) cc_final: 0.7986 (ptm) REVERT: D 824 MET cc_start: 0.7488 (mtm) cc_final: 0.7171 (mtm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1325 time to fit residues: 6.7146 Evaluate side-chains 32 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.540 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.7644 (mpp) cc_final: 0.7386 (mpp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0864 time to fit residues: 0.6104 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.154 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.158 Fit side-chains REVERT: N 179 MET cc_start: 0.1768 (tmm) cc_final: 0.1545 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0856 time to fit residues: 0.5547 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 317 optimal weight: 6.9990 chunk 216 optimal weight: 0.4980 chunk 5 optimal weight: 0.0970 chunk 283 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 324 optimal weight: 0.9990 chunk 263 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 341 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 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: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31998 Z= 0.266 Angle : 0.905 21.304 43364 Z= 0.467 Chirality : 0.058 1.089 4858 Planarity : 0.008 0.135 5514 Dihedral : 7.221 59.753 4282 Min Nonbonded Distance : 0.748 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.55 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % 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: -3.34 (0.12), residues: 3930 helix: -1.79 (0.12), residues: 1272 sheet: -2.30 (0.18), residues: 666 loop : -2.45 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP C 151 HIS 0.040 0.003 HIS A 314 PHE 0.058 0.003 PHE C 630 TYR 0.067 0.003 TYR C 88 ARG 0.081 0.002 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 5 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 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8640 (mmm) cc_final: 0.8387 (mmm) REVERT: A 375 MET cc_start: 0.7460 (mpp) cc_final: 0.7153 (mpp) REVERT: A 576 MET cc_start: 0.8421 (mtm) cc_final: 0.8087 (mmm) REVERT: A 839 MET cc_start: 0.8589 (ptt) cc_final: 0.8052 (ppp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1551 time to fit residues: 6.7848 Evaluate side-chains 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.735 Evaluate side-chains 33 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 142 MET cc_start: 0.7743 (mtt) cc_final: 0.7184 (tpt) REVERT: D 307 MET cc_start: 0.9165 (tmm) cc_final: 0.8821 (ppp) REVERT: D 388 TYR cc_start: 0.8511 (m-80) cc_final: 0.8295 (m-80) REVERT: D 465 LEU cc_start: 0.9505 (tp) cc_final: 0.9270 (tp) REVERT: D 654 MET cc_start: 0.8405 (ptt) cc_final: 0.7986 (ptm) REVERT: D 824 MET cc_start: 0.7488 (mtm) cc_final: 0.7171 (mtm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1525 time to fit residues: 7.6933 Evaluate side-chains 32 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.695 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.7644 (mpp) cc_final: 0.7386 (mpp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1124 time to fit residues: 0.7946 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.176 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.182 Fit side-chains REVERT: N 179 MET cc_start: 0.1768 (tmm) cc_final: 0.1545 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0898 time to fit residues: 0.6076 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 128 optimal weight: 1.9990 chunk 342 optimal weight: 0.8980 chunk 75 optimal weight: 0.0010 chunk 223 optimal weight: 10.0000 chunk 94 optimal weight: 0.0020 chunk 381 optimal weight: 8.9990 chunk 316 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 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: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31998 Z= 0.266 Angle : 0.905 21.304 43364 Z= 0.467 Chirality : 0.058 1.089 4858 Planarity : 0.008 0.135 5514 Dihedral : 7.221 59.753 4282 Min Nonbonded Distance : 0.748 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.55 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % 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: -3.34 (0.12), residues: 3930 helix: -1.79 (0.12), residues: 1272 sheet: -2.30 (0.18), residues: 666 loop : -2.45 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP C 151 HIS 0.040 0.003 HIS A 314 PHE 0.058 0.003 PHE A 630 TYR 0.067 0.003 TYR C 88 ARG 0.081 0.002 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 6 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 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8640 (mmm) cc_final: 0.8387 (mmm) REVERT: A 375 MET cc_start: 0.7460 (mpp) cc_final: 0.7153 (mpp) REVERT: A 576 MET cc_start: 0.8420 (mtm) cc_final: 0.8087 (mmm) REVERT: A 839 MET cc_start: 0.8588 (ptt) cc_final: 0.8052 (ppp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1600 time to fit residues: 7.0760 Evaluate side-chains 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.750 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 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 142 MET cc_start: 0.7743 (mtt) cc_final: 0.7184 (tpt) REVERT: D 307 MET cc_start: 0.9165 (tmm) cc_final: 0.8821 (ppp) REVERT: D 388 TYR cc_start: 0.8511 (m-80) cc_final: 0.8295 (m-80) REVERT: D 465 LEU cc_start: 0.9505 (tp) cc_final: 0.9270 (tp) REVERT: D 654 MET cc_start: 0.8405 (ptt) cc_final: 0.7986 (ptm) REVERT: D 824 MET cc_start: 0.7488 (mtm) cc_final: 0.7171 (mtm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1596 time to fit residues: 8.0651 Evaluate side-chains 32 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.749 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.7644 (mpp) cc_final: 0.7386 (mpp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1158 time to fit residues: 0.8214 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.189 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.196 Fit side-chains REVERT: N 179 MET cc_start: 0.1768 (tmm) cc_final: 0.1545 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1002 time to fit residues: 0.6595 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 10.0000 chunk 42 optimal weight: 0.0020 chunk 217 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 379 optimal weight: 2.9990 chunk 237 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 175 optimal weight: 0.0270 overall best weight: 2.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 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: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 31998 Z= 0.260 Angle : 0.907 17.845 43364 Z= 0.469 Chirality : 0.064 1.417 4858 Planarity : 0.009 0.179 5514 Dihedral : 7.287 57.748 4282 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.75 % Favored : 90.99 % Rotamer: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.42 % 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: -3.40 (0.12), residues: 3930 helix: -1.86 (0.12), residues: 1268 sheet: -2.25 (0.18), residues: 658 loop : -2.51 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.005 TRP B 610 HIS 0.056 0.004 HIS A 314 PHE 0.061 0.003 PHE A 630 TYR 0.068 0.003 TYR A 114 ARG 0.091 0.002 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 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 29 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8488 (mmm) cc_final: 0.8247 (mmm) REVERT: A 375 MET cc_start: 0.7602 (mpp) cc_final: 0.7075 (mpp) REVERT: A 576 MET cc_start: 0.8412 (mtm) cc_final: 0.8078 (mmm) REVERT: A 839 MET cc_start: 0.8413 (ptt) cc_final: 0.7896 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1494 time to fit residues: 6.8547 Evaluate side-chains 27 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.675 Evaluate side-chains 34 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: D 142 MET cc_start: 0.7757 (mtt) cc_final: 0.7209 (tpt) REVERT: D 307 MET cc_start: 0.9189 (tmm) cc_final: 0.8843 (ppp) REVERT: D 465 LEU cc_start: 0.9452 (tp) cc_final: 0.9196 (tp) REVERT: D 562 MET cc_start: 0.9471 (ptp) cc_final: 0.9210 (ptp) REVERT: D 654 MET cc_start: 0.8527 (ptt) cc_final: 0.8217 (ptm) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1439 time to fit residues: 7.4376 Evaluate side-chains 31 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.640 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.171 Fit side-chains REVERT: H 34 MET cc_start: 0.7614 (mpp) cc_final: 0.6894 (mpp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1094 time to fit residues: 0.7537 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.181 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.154 Fit side-chains REVERT: N 179 MET cc_start: 0.1793 (tmm) cc_final: 0.1584 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1005 time to fit residues: 0.6241 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 0.8980 chunk 151 optimal weight: 20.0000 chunk 226 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 73 optimal weight: 20.0000 chunk 241 optimal weight: 0.2980 chunk 258 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 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: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 31998 Z= 0.266 Angle : 0.902 17.508 43364 Z= 0.467 Chirality : 0.063 1.396 4858 Planarity : 0.009 0.179 5514 Dihedral : 7.285 57.791 4282 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.80 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.42 % 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: -3.40 (0.12), residues: 3930 helix: -1.86 (0.12), residues: 1268 sheet: -2.25 (0.18), residues: 658 loop : -2.51 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.005 TRP B 610 HIS 0.056 0.004 HIS A 314 PHE 0.061 0.003 PHE A 838 TYR 0.067 0.003 TYR C 114 ARG 0.088 0.002 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 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 29 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8490 (mmm) cc_final: 0.8248 (mmm) REVERT: A 375 MET cc_start: 0.7622 (mpp) cc_final: 0.7069 (mpp) REVERT: A 576 MET cc_start: 0.8414 (mtm) cc_final: 0.8079 (mmm) REVERT: A 839 MET cc_start: 0.8415 (ptt) cc_final: 0.7898 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1570 time to fit residues: 7.1149 Evaluate side-chains 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.738 Evaluate side-chains 33 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: D 142 MET cc_start: 0.7759 (mtt) cc_final: 0.7211 (tpt) REVERT: D 307 MET cc_start: 0.9187 (tmm) cc_final: 0.8842 (ppp) REVERT: D 465 LEU cc_start: 0.9453 (tp) cc_final: 0.9200 (tp) REVERT: D 562 MET cc_start: 0.9495 (ptp) cc_final: 0.9211 (ptp) REVERT: D 654 MET cc_start: 0.8524 (ptt) cc_final: 0.8212 (ptm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1546 time to fit residues: 7.8027 Evaluate side-chains 31 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.701 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.185 Fit side-chains REVERT: H 34 MET cc_start: 0.7634 (mpp) cc_final: 0.6893 (mpp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1232 time to fit residues: 0.8519 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.194 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 Fit side-chains REVERT: N 179 MET cc_start: 0.1792 (tmm) cc_final: 0.1583 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0923 time to fit residues: 0.6258 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 0.6980 chunk 363 optimal weight: 0.3980 chunk 331 optimal weight: 0.0670 chunk 353 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 319 optimal weight: 0.0370 chunk 334 optimal weight: 0.4980 chunk 352 optimal weight: 30.0000 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 730 HIS Total number of N/Q/H flips: 2 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: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 31998 Z= 0.279 Angle : 0.938 17.325 43364 Z= 0.477 Chirality : 0.064 1.161 4858 Planarity : 0.009 0.187 5514 Dihedral : 7.300 57.655 4282 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.21 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.42 % 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: -3.46 (0.12), residues: 3930 helix: -1.91 (0.12), residues: 1266 sheet: -2.31 (0.17), residues: 702 loop : -2.54 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.005 TRP A 151 HIS 0.055 0.004 HIS C 314 PHE 0.064 0.003 PHE A 838 TYR 0.067 0.003 TYR A 114 ARG 0.087 0.002 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 9 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 29 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8482 (mmm) cc_final: 0.8270 (mmm) REVERT: A 375 MET cc_start: 0.7927 (mpp) cc_final: 0.7390 (mpp) REVERT: A 576 MET cc_start: 0.8384 (mtm) cc_final: 0.8053 (mmm) REVERT: A 655 MET cc_start: 0.8443 (mmp) cc_final: 0.8184 (mmm) REVERT: A 839 MET cc_start: 0.8404 (ptt) cc_final: 0.7876 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1530 time to fit residues: 6.9313 Evaluate side-chains 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.672 Evaluate side-chains 33 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 142 MET cc_start: 0.7756 (mtt) cc_final: 0.7204 (tpt) REVERT: D 307 MET cc_start: 0.9174 (tmm) cc_final: 0.8835 (ppp) REVERT: D 654 MET cc_start: 0.8514 (ptt) cc_final: 0.8209 (ptm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1556 time to fit residues: 7.8252 Evaluate side-chains 31 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.782 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1187 time to fit residues: 0.8253 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.206 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.189 Fit side-chains REVERT: N 179 MET cc_start: 0.1791 (tmm) cc_final: 0.1587 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0935 time to fit residues: 0.6271 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 10.0000 chunk 374 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 chunk 177 optimal weight: 0.0670 chunk 260 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 chunk 361 optimal weight: 50.0000 chunk 312 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 241 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 730 HIS Total number of N/Q/H flips: 2 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: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 31998 Z= 0.286 Angle : 0.938 17.325 43364 Z= 0.478 Chirality : 0.064 1.161 4858 Planarity : 0.009 0.187 5514 Dihedral : 7.300 57.655 4282 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.21 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.16 % Twisted Proline : 1.19 % Twisted General : 0.42 % 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: -3.46 (0.12), residues: 3930 helix: -1.91 (0.12), residues: 1266 sheet: -2.31 (0.17), residues: 702 loop : -2.54 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.005 TRP A 151 HIS 0.055 0.004 HIS C 314 PHE 0.064 0.003 PHE A 838 TYR 0.067 0.003 TYR C 114 ARG 0.087 0.002 ARG C 156 ********************** REFINEMENT MACRO_CYCLE 10 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 28 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8481 (mmm) cc_final: 0.8270 (mmm) REVERT: A 375 MET cc_start: 0.7925 (mpp) cc_final: 0.7389 (mpp) REVERT: A 576 MET cc_start: 0.8384 (mtm) cc_final: 0.8052 (mmm) REVERT: A 655 MET cc_start: 0.8446 (mmp) cc_final: 0.8185 (mmm) REVERT: A 839 MET cc_start: 0.8404 (ptt) cc_final: 0.7877 (ppp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1651 time to fit residues: 7.1864 Evaluate side-chains 27 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.727 Evaluate side-chains 33 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 142 MET cc_start: 0.7756 (mtt) cc_final: 0.7204 (tpt) REVERT: D 307 MET cc_start: 0.9176 (tmm) cc_final: 0.8835 (ppp) REVERT: D 388 TYR cc_start: 0.8532 (m-80) cc_final: 0.8310 (m-80) REVERT: D 654 MET cc_start: 0.8510 (ptt) cc_final: 0.8210 (ptm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1564 time to fit residues: 7.8558 Evaluate side-chains 30 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.699 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1252 time to fit residues: 0.8522 Evaluate side-chains 4 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.188 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.195 Fit side-chains REVERT: N 179 MET cc_start: 0.1791 (tmm) cc_final: 0.1586 (tmm) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0965 time to fit residues: 0.6371 Evaluate side-chains 3 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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: 50.7473 > 50: distance: 1 - 4: 3.241 distance: 5 - 6: 3.325 distance: 6 - 7: 4.097 distance: 7 - 8: 5.548 distance: 10 - 13: 3.983 distance: 11 - 12: 9.978 distance: 11 - 18: 6.169 distance: 13 - 14: 5.214 distance: 16 - 17: 5.409 distance: 18 - 19: 3.969 distance: 19 - 20: 5.181 distance: 19 - 22: 6.095 distance: 20 - 21: 11.457 distance: 20 - 27: 7.045 distance: 22 - 23: 10.431 distance: 23 - 24: 6.710 distance: 24 - 25: 15.255 distance: 24 - 26: 7.925 distance: 28 - 31: 3.556 distance: 29 - 30: 4.155 distance: 29 - 41: 3.442 distance: 31 - 32: 5.362 distance: 32 - 33: 3.866 distance: 35 - 36: 3.940 distance: 41 - 42: 4.959 distance: 42 - 43: 14.880 distance: 42 - 45: 16.461 distance: 43 - 44: 11.456 distance: 43 - 49: 31.968 distance: 45 - 46: 9.861 distance: 46 - 47: 14.792 distance: 46 - 48: 16.343 distance: 49 - 50: 34.015 distance: 50 - 51: 28.911 distance: 51 - 52: 27.390 distance: 51 - 53: 26.442 distance: 53 - 54: 17.306 distance: 54 - 55: 10.192 distance: 54 - 57: 19.529 distance: 55 - 56: 14.734 distance: 55 - 61: 10.134 distance: 57 - 58: 9.669 distance: 58 - 59: 23.870 distance: 59 - 60: 23.793 distance: 61 - 62: 11.025 distance: 62 - 63: 9.911 distance: 62 - 65: 5.927 distance: 63 - 64: 23.909 distance: 63 - 69: 7.635 distance: 65 - 66: 9.564 distance: 66 - 67: 8.486 distance: 67 - 68: 5.878 distance: 69 - 70: 17.362 distance: 70 - 71: 13.150 distance: 71 - 72: 17.164 distance: 71 - 73: 15.552 distance: 73 - 74: 7.477 distance: 74 - 75: 11.080 distance: 74 - 77: 8.063 distance: 75 - 76: 10.394 distance: 77 - 78: 5.992 distance: 78 - 79: 9.230 distance: 79 - 80: 11.425