Starting phenix.real_space_refine on Mon Sep 23 19:25:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/09_2024/6hv9_0288.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/09_2024/6hv9_0288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/09_2024/6hv9_0288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/09_2024/6hv9_0288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/09_2024/6hv9_0288.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/09_2024/6hv9_0288.cif" } resolution = 4.98 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= 0.035 sd= 0.184 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 54 5.49 5 S 199 5.16 5 C 29962 2.51 5 N 8250 2.21 5 O 9150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 47617 Number of models: 1 Model: "" Number of chains: 18 Chain: "3" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4270 Classifications: {'peptide': 558} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 535} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "4" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4543 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 10 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "5" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4690 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 603} Chain breaks: 14 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 185 Chain: "6" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4307 Classifications: {'peptide': 571} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 62} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 550} Chain breaks: 9 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "2" Number of atoms: 4184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4184 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 19, 'TRANS': 529} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 104 Chain: "7" Number of atoms: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4785 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 586} Chain breaks: 13 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1492 Classifications: {'peptide': 194} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 28} Link IDs: {'CIS': 11, 'PTRANS': 3, 'TRANS': 179} Chain breaks: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1461 Classifications: {'peptide': 181} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 12} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1262 Classifications: {'peptide': 159} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 145} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1743 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 8, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 5 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 4239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4239 Classifications: {'peptide': 541} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 508} Chain breaks: 7 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "X" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3661 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 436} Chain breaks: 11 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5918 Classifications: {'peptide': 771} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 92} Link IDs: {'CIS': 4, 'PTRANS': 28, 'TRANS': 738} Chain breaks: 9 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 224 Chain: "5" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 46678 SG CYS A2108 141.943 44.627 62.060 1.00194.16 S ATOM 46705 SG CYS A2111 140.563 42.890 62.222 1.00201.20 S ATOM 46814 SG CYS A2130 141.002 43.072 64.673 1.00205.54 S ATOM 46838 SG CYS A2133 143.942 41.763 61.740 1.00208.50 S ATOM 47101 SG CYS A2164 112.564 72.569 89.689 1.00127.78 S ATOM 47124 SG CYS A2167 110.107 72.637 87.810 1.00131.93 S ATOM 47225 SG CYS A2179 109.162 74.225 88.617 1.00116.92 S ATOM 47238 SG CYS A2181 108.509 73.695 90.044 1.00115.72 S Time building chain proxies: 19.88, per 1000 atoms: 0.42 Number of scatterers: 47617 At special positions: 0 Unit cell: (218.04, 169.74, 242.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 199 16.00 P 54 15.00 O 9150 8.00 N 8250 7.00 C 29962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.88 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2111 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2133 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2130 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2108 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2167 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2181 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2164 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2179 " Number of angles added : 12 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11518 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 45 sheets defined 44.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain '3' and resid 19 through 35 Processing helix chain '3' and resid 36 through 56 removed outlier: 3.773A pdb=" N SER 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 121 through 137 Processing helix chain '3' and resid 261 through 265 removed outlier: 3.553A pdb=" N MET 3 264 " --> pdb=" O MET 3 261 " (cutoff:3.500A) Processing helix chain '3' and resid 279 through 283 removed outlier: 3.609A pdb=" N VAL 3 283 " --> pdb=" O ASP 3 280 " (cutoff:3.500A) Processing helix chain '3' and resid 344 through 354 Processing helix chain '3' and resid 358 through 367 Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 418 through 426 Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 482 through 493 removed outlier: 4.020A pdb=" N HIS 3 487 " --> pdb=" O ARG 3 483 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN 3 493 " --> pdb=" O VAL 3 489 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 543 removed outlier: 3.890A pdb=" N LEU 3 540 " --> pdb=" O PRO 3 536 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER 3 541 " --> pdb=" O ASP 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 652 through 667 removed outlier: 3.541A pdb=" N ARG 3 657 " --> pdb=" O ILE 3 653 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG 3 666 " --> pdb=" O TYR 3 662 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL 3 667 " --> pdb=" O ALA 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 689 removed outlier: 3.860A pdb=" N ASN 3 677 " --> pdb=" O GLN 3 673 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE 3 679 " --> pdb=" O ALA 3 675 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS 3 681 " --> pdb=" O ASN 3 677 " (cutoff:3.500A) Processing helix chain '3' and resid 690 through 693 Processing helix chain '3' and resid 698 through 716 removed outlier: 3.772A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA 3 709 " --> pdb=" O LEU 3 705 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 737 removed outlier: 3.755A pdb=" N ALA 3 726 " --> pdb=" O ASN 3 722 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN 3 731 " --> pdb=" O LYS 3 727 " (cutoff:3.500A) Processing helix chain '4' and resid 186 through 199 removed outlier: 3.705A pdb=" N CYS 4 190 " --> pdb=" O SER 4 186 " (cutoff:3.500A) Processing helix chain '4' and resid 203 through 210 Processing helix chain '4' and resid 224 through 235 removed outlier: 4.263A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) Processing helix chain '4' and resid 245 through 251 removed outlier: 3.590A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR 4 251 " --> pdb=" O ASN 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.535A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 3.558A pdb=" N VAL 4 268 " --> pdb=" O TYR 4 264 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE 4 269 " --> pdb=" O PRO 4 265 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 299 Processing helix chain '4' and resid 422 through 424 No H-bonds generated for 'chain '4' and resid 422 through 424' Processing helix chain '4' and resid 505 through 514 Processing helix chain '4' and resid 517 through 525 removed outlier: 4.239A pdb=" N ALA 4 523 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 545 removed outlier: 3.890A pdb=" N LEU 4 544 " --> pdb=" O ILE 4 540 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 634 through 637 removed outlier: 3.769A pdb=" N MET 4 637 " --> pdb=" O PHE 4 634 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 634 through 637' Processing helix chain '4' and resid 644 through 651 removed outlier: 3.831A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 700 Processing helix chain '4' and resid 714 through 729 Processing helix chain '4' and resid 730 through 732 No H-bonds generated for 'chain '4' and resid 730 through 732' Processing helix chain '4' and resid 745 through 757 removed outlier: 3.546A pdb=" N SER 4 752 " --> pdb=" O THR 4 748 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU 4 756 " --> pdb=" O SER 4 752 " (cutoff:3.500A) Processing helix chain '4' and resid 764 through 780 removed outlier: 3.736A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY 4 776 " --> pdb=" O ARG 4 772 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET 4 780 " --> pdb=" O GLY 4 776 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 811 removed outlier: 3.720A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU 4 806 " --> pdb=" O ILE 4 802 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA 4 807 " --> pdb=" O ARG 4 803 " (cutoff:3.500A) Processing helix chain '4' and resid 821 through 835 removed outlier: 3.871A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) Processing helix chain '5' and resid 24 through 36 removed outlier: 3.897A pdb=" N ILE 5 28 " --> pdb=" O ASN 5 24 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 57 removed outlier: 4.175A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 73 through 82 removed outlier: 3.638A pdb=" N GLU 5 82 " --> pdb=" O LYS 5 78 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 105 Proline residue: 5 88 - end of helix removed outlier: 3.553A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 352 through 362 removed outlier: 3.560A pdb=" N ARG 5 362 " --> pdb=" O LEU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 371 Processing helix chain '5' and resid 381 through 392 removed outlier: 4.167A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS 5 390 " --> pdb=" O LYS 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 421 through 433 removed outlier: 3.540A pdb=" N SER 5 433 " --> pdb=" O VAL 5 429 " (cutoff:3.500A) Processing helix chain '5' and resid 457 through 461 removed outlier: 3.588A pdb=" N GLU 5 461 " --> pdb=" O MET 5 458 " (cutoff:3.500A) Processing helix chain '5' and resid 489 through 497 removed outlier: 3.807A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET 5 497 " --> pdb=" O ILE 5 493 " (cutoff:3.500A) Processing helix chain '5' and resid 527 through 533 removed outlier: 3.709A pdb=" N TYR 5 530 " --> pdb=" O TYR 5 527 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP 5 531 " --> pdb=" O GLY 5 528 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP 5 532 " --> pdb=" O ARG 5 529 " (cutoff:3.500A) Processing helix chain '5' and resid 544 through 549 Processing helix chain '5' and resid 561 through 577 Processing helix chain '5' and resid 585 through 592 Processing helix chain '5' and resid 595 through 610 removed outlier: 3.523A pdb=" N MET 5 599 " --> pdb=" O SER 5 595 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU 5 608 " --> pdb=" O THR 5 604 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS 5 609 " --> pdb=" O TYR 5 605 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS 5 610 " --> pdb=" O CYS 5 606 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 639 removed outlier: 4.418A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL 5 627 " --> pdb=" O SER 5 623 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR 5 628 " --> pdb=" O SER 5 624 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU 5 639 " --> pdb=" O ILE 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 668 removed outlier: 4.028A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG 5 658 " --> pdb=" O GLU 5 654 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE 5 659 " --> pdb=" O ALA 5 655 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR 5 660 " --> pdb=" O ILE 5 656 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 693 removed outlier: 4.242A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE 5 681 " --> pdb=" O VAL 5 677 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG 5 682 " --> pdb=" O ASP 5 678 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) Processing helix chain '5' and resid 717 through 722 Processing helix chain '5' and resid 729 through 739 Processing helix chain '5' and resid 744 through 753 Processing helix chain '5' and resid 760 through 774 removed outlier: 4.033A pdb=" N ARG 5 764 " --> pdb=" O THR 5 760 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR 5 771 " --> pdb=" O GLY 5 767 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG 5 772 " --> pdb=" O GLN 5 768 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 121 Processing helix chain '6' and resid 134 through 147 Processing helix chain '6' and resid 154 through 159 removed outlier: 3.585A pdb=" N LEU 6 158 " --> pdb=" O ASP 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 166 through 171 Processing helix chain '6' and resid 174 through 176 No H-bonds generated for 'chain '6' and resid 174 through 176' Processing helix chain '6' and resid 177 through 193 Processing helix chain '6' and resid 275 through 279 removed outlier: 3.529A pdb=" N ILE 6 279 " --> pdb=" O ILE 6 276 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 513 through 521 Processing helix chain '6' and resid 524 through 532 removed outlier: 3.770A pdb=" N ARG 6 531 " --> pdb=" O ASP 6 527 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 551 Processing helix chain '6' and resid 580 through 592 removed outlier: 3.603A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 644 Processing helix chain '6' and resid 645 through 658 removed outlier: 3.695A pdb=" N GLN 6 649 " --> pdb=" O ASP 6 645 " (cutoff:3.500A) Processing helix chain '6' and resid 695 through 700 removed outlier: 3.572A pdb=" N LEU 6 699 " --> pdb=" O LEU 6 695 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN 6 700 " --> pdb=" O ARG 6 696 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 695 through 700' Processing helix chain '6' and resid 702 through 709 Processing helix chain '6' and resid 720 through 736 Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 769 through 783 removed outlier: 3.575A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 814 removed outlier: 3.767A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA 6 811 " --> pdb=" O SER 6 807 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 840 removed outlier: 3.886A pdb=" N VAL 6 838 " --> pdb=" O SER 6 834 " (cutoff:3.500A) Processing helix chain '2' and resid 203 through 211 removed outlier: 4.167A pdb=" N ARG 2 209 " --> pdb=" O ARG 2 205 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU 2 210 " --> pdb=" O THR 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 238 removed outlier: 4.114A pdb=" N ARG 2 232 " --> pdb=" O GLY 2 228 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR 2 233 " --> pdb=" O ALA 2 229 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 253 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 263 through 281 removed outlier: 3.854A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU 2 268 " --> pdb=" O PRO 2 264 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 Processing helix chain '2' and resid 478 through 489 removed outlier: 3.846A pdb=" N PHE 2 484 " --> pdb=" O GLU 2 480 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE 2 487 " --> pdb=" O GLU 2 483 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 500 removed outlier: 3.651A pdb=" N LYS 2 496 " --> pdb=" O GLY 2 492 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE 2 498 " --> pdb=" O ILE 2 494 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 removed outlier: 3.585A pdb=" N PHE 2 520 " --> pdb=" O ALA 2 516 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY 2 521 " --> pdb=" O CYS 2 517 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 560 removed outlier: 3.578A pdb=" N ILE 2 552 " --> pdb=" O ALA 2 548 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 removed outlier: 3.715A pdb=" N LEU 2 598 " --> pdb=" O GLY 2 594 " (cutoff:3.500A) Processing helix chain '2' and resid 608 through 612 Processing helix chain '2' and resid 613 through 626 Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 670 through 677 removed outlier: 3.596A pdb=" N LEU 2 674 " --> pdb=" O THR 2 670 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE 2 677 " --> pdb=" O ILE 2 673 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 704 Processing helix chain '2' and resid 759 through 774 removed outlier: 3.587A pdb=" N THR 2 772 " --> pdb=" O HIS 2 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS 2 773 " --> pdb=" O TYR 2 769 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 797 removed outlier: 4.179A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 825 removed outlier: 3.729A pdb=" N GLU 2 811 " --> pdb=" O VAL 2 807 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER 2 819 " --> pdb=" O ARG 2 815 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE 2 820 " --> pdb=" O ILE 2 816 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA 2 821 " --> pdb=" O ALA 2 817 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 removed outlier: 3.666A pdb=" N LEU 2 834 " --> pdb=" O SER 2 830 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP 2 843 " --> pdb=" O LYS 2 839 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER 2 844 " --> pdb=" O VAL 2 840 " (cutoff:3.500A) Processing helix chain '2' and resid 848 through 849 No H-bonds generated for 'chain '2' and resid 848 through 849' Processing helix chain '2' and resid 850 through 852 No H-bonds generated for 'chain '2' and resid 850 through 852' Processing helix chain '2' and resid 853 through 858 Processing helix chain '7' and resid 15 through 27 Processing helix chain '7' and resid 61 through 72 removed outlier: 3.537A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) Processing helix chain '7' and resid 84 through 96 Processing helix chain '7' and resid 102 through 109 removed outlier: 3.640A pdb=" N ASN 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 119 removed outlier: 4.386A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU 7 116 " --> pdb=" O HIS 7 112 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE 7 117 " --> pdb=" O PHE 7 113 " (cutoff:3.500A) Processing helix chain '7' and resid 120 through 124 Processing helix chain '7' and resid 126 through 130 removed outlier: 3.711A pdb=" N THR 7 129 " --> pdb=" O PRO 7 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS 7 130 " --> pdb=" O LEU 7 127 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 126 through 130' Processing helix chain '7' and resid 137 through 144 removed outlier: 4.105A pdb=" N VAL 7 141 " --> pdb=" O ASP 7 137 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 215 removed outlier: 3.590A pdb=" N ALA 7 212 " --> pdb=" O SER 7 208 " (cutoff:3.500A) Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 395 through 406 removed outlier: 3.759A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 removed outlier: 3.592A pdb=" N ALA 7 415 " --> pdb=" O TYR 7 411 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 removed outlier: 3.675A pdb=" N GLY 7 438 " --> pdb=" O LEU 7 434 " (cutoff:3.500A) Processing helix chain '7' and resid 464 through 464 No H-bonds generated for 'chain '7' and resid 464 through 464' Processing helix chain '7' and resid 466 through 468 No H-bonds generated for 'chain '7' and resid 466 through 468' Processing helix chain '7' and resid 469 through 477 removed outlier: 3.992A pdb=" N CYS 7 474 " --> pdb=" O LEU 7 470 " (cutoff:3.500A) Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 526 through 529 Processing helix chain '7' and resid 530 through 542 removed outlier: 3.747A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 587 through 594 removed outlier: 3.724A pdb=" N LEU 7 591 " --> pdb=" O PRO 7 587 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 622 removed outlier: 4.287A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU 7 612 " --> pdb=" O ASP 7 608 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 646 Processing helix chain '7' and resid 654 through 672 removed outlier: 3.623A pdb=" N VAL 7 661 " --> pdb=" O ASN 7 657 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN 7 662 " --> pdb=" O ASP 7 658 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 702 removed outlier: 3.989A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 724 removed outlier: 3.563A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA 7 716 " --> pdb=" O ASP 7 712 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL 7 720 " --> pdb=" O ALA 7 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.564A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 58 removed outlier: 3.806A pdb=" N ILE C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 104 removed outlier: 3.654A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 145 removed outlier: 3.609A pdb=" N GLN C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 202 removed outlier: 3.801A pdb=" N ARG C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 21 Processing helix chain 'D' and resid 73 through 82 Processing helix chain 'D' and resid 94 through 107 Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.524A pdb=" N ASN D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 133 Processing helix chain 'D' and resid 140 through 161 removed outlier: 3.625A pdb=" N LYS D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 200 removed outlier: 3.552A pdb=" N ILE D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Proline residue: D 183 - end of helix removed outlier: 3.948A pdb=" N ASP D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.635A pdb=" N VAL E 9 " --> pdb=" O ASP E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 55 removed outlier: 3.922A pdb=" N ILE E 53 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 80 Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.925A pdb=" N ASP E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 4.610A pdb=" N ILE E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 removed outlier: 4.104A pdb=" N LYS E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 140 removed outlier: 4.250A pdb=" N GLU E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER E 140 " --> pdb=" O ASN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 Processing helix chain 'E' and resid 170 through 192 removed outlier: 3.579A pdb=" N PHE E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 73 Processing helix chain 'F' and resid 80 through 97 removed outlier: 4.498A pdb=" N ARG F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 removed outlier: 3.810A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 123 through 164 removed outlier: 5.740A pdb=" N LEU F 156 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR F 157 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 198 removed outlier: 3.564A pdb=" N SER F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 208 removed outlier: 3.536A pdb=" N GLN F 207 " --> pdb=" O GLU F 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA F 208 " --> pdb=" O GLU F 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 204 through 208' Processing helix chain 'F' and resid 282 through 289 Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.620A pdb=" N ALA G 11 " --> pdb=" O GLN G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 52 removed outlier: 3.858A pdb=" N LEU G 39 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 72 removed outlier: 3.912A pdb=" N ARG G 69 " --> pdb=" O SER G 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 130 through 135 removed outlier: 3.925A pdb=" N ILE G 134 " --> pdb=" O ASN G 130 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 130 through 135' Processing helix chain 'G' and resid 153 through 160 removed outlier: 3.926A pdb=" N GLU G 157 " --> pdb=" O GLY G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 240 removed outlier: 3.818A pdb=" N GLU G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 262 removed outlier: 4.221A pdb=" N GLN G 254 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 280 removed outlier: 3.704A pdb=" N LEU G 280 " --> pdb=" O GLY G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 302 Proline residue: G 293 - end of helix removed outlier: 3.655A pdb=" N GLU G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 340 Processing helix chain 'G' and resid 341 through 349 removed outlier: 4.194A pdb=" N ALA G 346 " --> pdb=" O ASN G 342 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS G 347 " --> pdb=" O TYR G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 367 removed outlier: 4.002A pdb=" N LYS G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG G 358 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 375 removed outlier: 3.506A pdb=" N GLU G 375 " --> pdb=" O SER G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 387 Processing helix chain 'G' and resid 387 through 396 Processing helix chain 'G' and resid 397 through 400 Processing helix chain 'G' and resid 421 through 434 Processing helix chain 'G' and resid 463 through 484 removed outlier: 3.737A pdb=" N TRP G 478 " --> pdb=" O VAL G 474 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU G 479 " --> pdb=" O SER G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 517 removed outlier: 4.083A pdb=" N LEU G 492 " --> pdb=" O LYS G 488 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN G 500 " --> pdb=" O ILE G 496 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 540 Processing helix chain 'G' and resid 541 through 557 removed outlier: 3.558A pdb=" N LEU G 545 " --> pdb=" O ASN G 541 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS G 555 " --> pdb=" O TRP G 551 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA G 557 " --> pdb=" O ILE G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 614 Processing helix chain 'G' and resid 633 through 646 Proline residue: G 639 - end of helix Processing helix chain 'B' and resid 13 through 23 Proline residue: B 19 - end of helix Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.614A pdb=" N GLN B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 90 removed outlier: 3.947A pdb=" N GLN B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 232 removed outlier: 4.280A pdb=" N PHE B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 221 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.758A pdb=" N LEU B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 384 through 394 removed outlier: 4.201A pdb=" N HIS B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 427 removed outlier: 3.830A pdb=" N ASP B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 Processing helix chain 'B' and resid 509 through 512 Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.869A pdb=" N LYS B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 Processing helix chain 'B' and resid 626 through 631 removed outlier: 3.610A pdb=" N LEU B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1370 Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 4.261A pdb=" N GLY A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1546 removed outlier: 3.963A pdb=" N LYS A1538 " --> pdb=" O GLN A1534 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A1541 " --> pdb=" O GLU A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1584 removed outlier: 3.929A pdb=" N LEU A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A1580 " --> pdb=" O GLU A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1598 through 1603 removed outlier: 3.581A pdb=" N GLY A1602 " --> pdb=" O THR A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 4.104A pdb=" N THR A1630 " --> pdb=" O ASN A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1636 Processing helix chain 'A' and resid 1636 through 1641 Processing helix chain 'A' and resid 1641 through 1654 Processing helix chain 'A' and resid 1668 through 1678 removed outlier: 4.261A pdb=" N ILE A1672 " --> pdb=" O MET A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1744 Processing helix chain 'A' and resid 1787 through 1800 removed outlier: 3.635A pdb=" N ASP A1800 " --> pdb=" O LYS A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1807 through 1814 removed outlier: 4.355A pdb=" N ASN A1814 " --> pdb=" O ASP A1810 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1820 Processing helix chain 'A' and resid 1831 through 1852 removed outlier: 3.710A pdb=" N HIS A1835 " --> pdb=" O LEU A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1881 through 1892 Processing helix chain 'A' and resid 1938 through 1943 Processing helix chain 'A' and resid 1949 through 1956 removed outlier: 3.751A pdb=" N PHE A1953 " --> pdb=" O TYR A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1971 removed outlier: 3.711A pdb=" N TYR A1971 " --> pdb=" O THR A1967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2003 Processing helix chain 'A' and resid 2005 through 2019 Proline residue: A2011 - end of helix Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 4.239A pdb=" N ALA A2034 " --> pdb=" O PRO A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2059 Proline residue: A2050 - end of helix removed outlier: 3.903A pdb=" N CYS A2059 " --> pdb=" O VAL A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2072 Processing helix chain 'A' and resid 2140 through 2158 Processing helix chain 'A' and resid 2190 through 2209 removed outlier: 3.984A pdb=" N ILE A2194 " --> pdb=" O PRO A2190 " (cutoff:3.500A) Processing helix chain 'A' and resid 2210 through 2221 Processing sheet with id=AA1, first strand: chain '3' and resid 193 through 196 removed outlier: 3.686A pdb=" N ARG 3 193 " --> pdb=" O HIS 3 253 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN 3 254 " --> pdb=" O LEU 3 278 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE 3 274 " --> pdb=" O VAL 3 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 193 through 196 removed outlier: 3.686A pdb=" N ARG 3 193 " --> pdb=" O HIS 3 253 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR 3 257 " --> pdb=" O THR 3 187 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN 3 259 " --> pdb=" O ILE 3 185 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN 3 293 " --> pdb=" O VAL 3 326 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL 3 326 " --> pdb=" O ASN 3 293 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL 3 295 " --> pdb=" O ASN 3 324 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN 3 324 " --> pdb=" O VAL 3 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 198 through 199 removed outlier: 3.511A pdb=" N ARG 3 212 " --> pdb=" O SER 3 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 201 through 203 Processing sheet with id=AA5, first strand: chain '3' and resid 429 through 433 removed outlier: 3.924A pdb=" N PHE 3 547 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 494 through 495 Processing sheet with id=AA7, first strand: chain '4' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain '4' and resid 325 through 328 removed outlier: 3.594A pdb=" N HIS 4 465 " --> pdb=" O THR 4 436 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '4' and resid 331 through 335 removed outlier: 7.119A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '4' and resid 331 through 335 removed outlier: 7.119A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 347 through 348 Processing sheet with id=AB3, first strand: chain '4' and resid 589 through 590 removed outlier: 6.069A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP 4 632 " --> pdb=" O VAL 4 589 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE 4 564 " --> pdb=" O ILE 4 671 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA 4 673 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 4 675 " --> pdb=" O LEU 4 566 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 606 through 607 Processing sheet with id=AB5, first strand: chain '5' and resid 61 through 64 removed outlier: 6.329A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '5' and resid 257 through 259 removed outlier: 6.595A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 189 through 193 removed outlier: 3.569A pdb=" N THR 5 190 " --> pdb=" O ILE 5 181 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '5' and resid 436 through 439 removed outlier: 6.458A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '5' and resid 501 through 503 Processing sheet with id=AC1, first strand: chain '6' and resid 293 through 295 removed outlier: 3.612A pdb=" N THR 6 295 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '6' and resid 293 through 295 removed outlier: 3.612A pdb=" N THR 6 295 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN 6 357 " --> pdb=" O LEU 6 381 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 6 381 " --> pdb=" O GLN 6 357 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA 6 456 " --> pdb=" O ILE 6 380 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG 6 382 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '6' and resid 403 through 404 removed outlier: 4.259A pdb=" N VAL 6 404 " --> pdb=" O LYS 6 451 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS 6 451 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '6' and resid 573 through 574 removed outlier: 3.537A pdb=" N ALA 6 682 " --> pdb=" O VAL 6 573 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL 6 596 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS 6 637 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR 6 598 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP 6 639 " --> pdb=" O THR 6 598 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '2' and resid 331 through 334 removed outlier: 3.907A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N THR 2 449 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR 2 325 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '2' and resid 336 through 338 Processing sheet with id=AC7, first strand: chain '2' and resid 539 through 542 removed outlier: 3.729A pdb=" N LEU 2 542 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '2' and resid 565 through 566 removed outlier: 3.602A pdb=" N ILE 2 647 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '7' and resid 268 through 272 removed outlier: 3.604A pdb=" N PHE 7 310 " --> pdb=" O LYS 7 252 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE 7 258 " --> pdb=" O ALA 7 304 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ALA 7 304 " --> pdb=" O ILE 7 258 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N TYR 7 260 " --> pdb=" O THR 7 302 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR 7 302 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) removed outlier: 13.692A pdb=" N SER 7 330 " --> pdb=" O THR 7 372 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N THR 7 374 " --> pdb=" O SER 7 330 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASN 7 332 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN 7 336 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N PHE 7 380 " --> pdb=" O ASN 7 336 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE 7 380 " --> pdb=" O THR 7 352 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE 7 348 " --> pdb=" O HIS 7 384 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL 7 349 " --> pdb=" O GLY 7 243 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '7' and resid 523 through 524 removed outlier: 6.480A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 162 through 163 Processing sheet with id=AD3, first strand: chain 'D' and resid 69 through 72 Processing sheet with id=AD4, first strand: chain 'E' and resid 15 through 17 Processing sheet with id=AD5, first strand: chain 'F' and resid 227 through 228 removed outlier: 3.632A pdb=" N MET F 277 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 231 through 232 Processing sheet with id=AD7, first strand: chain 'G' and resid 126 through 127 removed outlier: 3.514A pdb=" N THR G 246 " --> pdb=" O ARG G 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 319 through 320 removed outlier: 3.595A pdb=" N ARG G 411 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE G 419 " --> pdb=" O ARG G 411 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 581 through 582 Processing sheet with id=AE1, first strand: chain 'B' and resid 181 through 184 removed outlier: 4.105A pdb=" N SER B 182 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 189 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 339 through 340 removed outlier: 8.768A pdb=" N PHE B 339 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU B 306 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY B 303 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 300 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 305 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TRP B 296 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 431 through 433 removed outlier: 3.582A pdb=" N GLU B 674 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 683 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 676 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.832A pdb=" N ILE B 539 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 534 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU B 538 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL B 640 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 540 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N CYS B 642 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE B 542 " --> pdb=" O CYS B 642 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 639 " --> pdb=" O LYS B 657 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 659 " --> pdb=" O MET B 639 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 641 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1321 through 1327 removed outlier: 6.801A pdb=" N PHE A1339 " --> pdb=" O GLU A1323 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A1325 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU A1337 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1501 through 1503 removed outlier: 5.753A pdb=" N GLY A1485 " --> pdb=" O LEU A1591 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1734 through 1735 Processing sheet with id=AE8, first strand: chain 'A' and resid 2102 through 2106 removed outlier: 4.263A pdb=" N ASP A2105 " --> pdb=" O SER A2115 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER A2115 " --> pdb=" O ASP A2105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 2162 through 2163 1774 hydrogen bonds defined for protein. 5157 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: 15.15 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.26: 7979 1.26 - 1.43: 12016 1.43 - 1.60: 28072 1.60 - 1.78: 92 1.78 - 1.95: 271 Bond restraints: 48430 Sorted by residual: bond pdb=" C GLU 5 269 " pdb=" N MET 5 270 " ideal model delta sigma weight residual 1.339 1.086 0.253 5.57e-02 3.22e+02 2.06e+01 bond pdb=" CB GLU 2 622 " pdb=" CG GLU 2 622 " ideal model delta sigma weight residual 1.520 1.390 0.130 3.00e-02 1.11e+03 1.87e+01 bond pdb=" O5' DT J 3 " pdb=" C5' DT J 3 " ideal model delta sigma weight residual 1.423 1.547 -0.124 3.00e-02 1.11e+03 1.70e+01 bond pdb=" CB VAL 2 397 " pdb=" CG2 VAL 2 397 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.69e+01 bond pdb=" CA TYR 4 531 " pdb=" CB TYR 4 531 " ideal model delta sigma weight residual 1.530 1.597 -0.067 1.69e-02 3.50e+03 1.58e+01 ... (remaining 48425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 64201 5.29 - 10.59: 1365 10.59 - 15.88: 122 15.88 - 21.17: 8 21.17 - 26.47: 1 Bond angle restraints: 65697 Sorted by residual: angle pdb=" C VAL F 216 " pdb=" N ASN F 217 " pdb=" CA ASN F 217 " ideal model delta sigma weight residual 122.84 143.44 -20.60 1.81e+00 3.05e-01 1.30e+02 angle pdb=" C ILE G 98 " pdb=" N ASP G 99 " pdb=" CA ASP G 99 " ideal model delta sigma weight residual 121.80 148.27 -26.47 2.44e+00 1.68e-01 1.18e+02 angle pdb=" C LYS F 200 " pdb=" N TYR F 201 " pdb=" CA TYR F 201 " ideal model delta sigma weight residual 121.70 138.87 -17.17 1.80e+00 3.09e-01 9.10e+01 angle pdb=" C SER 5 444 " pdb=" CA SER 5 444 " pdb=" CB SER 5 444 " ideal model delta sigma weight residual 110.45 95.44 15.01 1.73e+00 3.34e-01 7.53e+01 angle pdb=" C ILE C 149 " pdb=" N ASP C 150 " pdb=" CA ASP C 150 " ideal model delta sigma weight residual 121.70 137.10 -15.40 1.80e+00 3.09e-01 7.32e+01 ... (remaining 65692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 29045 35.56 - 71.12: 394 71.12 - 106.68: 29 106.68 - 142.24: 4 142.24 - 177.80: 1 Dihedral angle restraints: 29473 sinusoidal: 11839 harmonic: 17634 Sorted by residual: dihedral pdb=" CA THR F 212 " pdb=" C THR F 212 " pdb=" N GLU F 213 " pdb=" CA GLU F 213 " ideal model delta harmonic sigma weight residual 180.00 53.84 126.16 0 5.00e+00 4.00e-02 6.37e+02 dihedral pdb=" CA VAL F 216 " pdb=" C VAL F 216 " pdb=" N ASN F 217 " pdb=" CA ASN F 217 " ideal model delta harmonic sigma weight residual 180.00 56.50 123.50 0 5.00e+00 4.00e-02 6.10e+02 dihedral pdb=" CA ILE G 98 " pdb=" C ILE G 98 " pdb=" N ASP G 99 " pdb=" CA ASP G 99 " ideal model delta harmonic sigma weight residual 180.00 68.58 111.42 0 5.00e+00 4.00e-02 4.97e+02 ... (remaining 29470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 6664 0.129 - 0.257: 933 0.257 - 0.386: 77 0.386 - 0.514: 5 0.514 - 0.643: 1 Chirality restraints: 7680 Sorted by residual: chirality pdb=" CA ARG B 669 " pdb=" N ARG B 669 " pdb=" C ARG B 669 " pdb=" CB ARG B 669 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ARG A1664 " pdb=" N ARG A1664 " pdb=" C ARG A1664 " pdb=" CB ARG A1664 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA PHE G 605 " pdb=" N PHE G 605 " pdb=" C PHE G 605 " pdb=" CB PHE G 605 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 7677 not shown) Planarity restraints: 8241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 523 " -0.219 9.50e-02 1.11e+02 1.24e-01 7.69e+01 pdb=" NE ARG G 523 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG G 523 " -0.143 2.00e-02 2.50e+03 pdb=" NH1 ARG G 523 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG G 523 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 212 " -0.035 2.00e-02 2.50e+03 6.89e-02 4.75e+01 pdb=" C THR F 212 " 0.119 2.00e-02 2.50e+03 pdb=" O THR F 212 " -0.044 2.00e-02 2.50e+03 pdb=" N GLU F 213 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 98 " -0.031 2.00e-02 2.50e+03 6.32e-02 3.99e+01 pdb=" C ILE G 98 " 0.109 2.00e-02 2.50e+03 pdb=" O ILE G 98 " -0.041 2.00e-02 2.50e+03 pdb=" N ASP G 99 " -0.038 2.00e-02 2.50e+03 ... (remaining 8238 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 2 2.14 - 2.83: 14205 2.83 - 3.52: 66833 3.52 - 4.21: 104476 4.21 - 4.90: 168063 Nonbonded interactions: 353579 Sorted by model distance: nonbonded pdb=" N CYS A2167 " pdb="ZN ZN A2302 " model vdw 1.447 2.310 nonbonded pdb=" O HIS 3 564 " pdb=" OG1 THR 3 568 " model vdw 2.137 3.040 nonbonded pdb=" O LEU 6 830 " pdb=" OG SER 6 834 " model vdw 2.161 3.040 nonbonded pdb=" O ARG 2 326 " pdb=" OG1 THR 2 389 " model vdw 2.197 3.040 nonbonded pdb=" O LEU A1739 " pdb=" OG1 THR A1743 " model vdw 2.205 3.040 ... (remaining 353574 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.700 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: 1.290 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 84.490 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.012 0.253 48430 Z= 0.756 Angle : 1.864 26.467 65697 Z= 1.021 Chirality : 0.088 0.643 7680 Planarity : 0.008 0.124 8241 Dihedral : 12.297 177.800 17955 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.90 % Favored : 88.79 % Rotamer: Outliers : 0.49 % Allowed : 3.97 % Favored : 95.55 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.02 (0.09), residues: 5814 helix: -2.63 (0.08), residues: 2286 sheet: -2.29 (0.19), residues: 610 loop : -2.78 (0.10), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.007 TRP A1645 HIS 0.035 0.006 HIS E 138 PHE 0.059 0.006 PHE C 190 TYR 0.060 0.005 TYR 5 59 ARG 0.146 0.002 ARG G 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 979 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8588 (t80) cc_final: 0.8266 (t80) REVERT: 3 318 LYS cc_start: 0.7684 (pttm) cc_final: 0.7025 (tttt) REVERT: 3 367 LEU cc_start: 0.8255 (mt) cc_final: 0.7638 (mp) REVERT: 3 471 CYS cc_start: 0.8980 (m) cc_final: 0.8395 (t) REVERT: 3 472 ILE cc_start: 0.9058 (mt) cc_final: 0.8823 (mm) REVERT: 3 545 LEU cc_start: 0.8029 (mt) cc_final: 0.7706 (mt) REVERT: 4 382 MET cc_start: 0.7658 (ttp) cc_final: 0.7430 (tpp) REVERT: 4 439 PHE cc_start: 0.8256 (t80) cc_final: 0.7895 (t80) REVERT: 4 637 MET cc_start: 0.7980 (mmt) cc_final: 0.7522 (mmm) REVERT: 5 65 MET cc_start: 0.8311 (ttp) cc_final: 0.7888 (ptt) REVERT: 5 69 ILE cc_start: 0.9379 (tp) cc_final: 0.8953 (tp) REVERT: 5 138 ILE cc_start: 0.7822 (mt) cc_final: 0.7500 (pt) REVERT: 5 270 MET cc_start: 0.7320 (mmp) cc_final: 0.7112 (mmm) REVERT: 5 271 PRO cc_start: 0.6372 (Cg_endo) cc_final: 0.5647 (Cg_exo) REVERT: 5 303 SER cc_start: 0.7877 (p) cc_final: 0.7584 (m) REVERT: 5 330 ILE cc_start: 0.8019 (mt) cc_final: 0.7753 (mp) REVERT: 5 370 LEU cc_start: 0.7471 (mp) cc_final: 0.7190 (mp) REVERT: 5 427 LYS cc_start: 0.7148 (mttp) cc_final: 0.6937 (tptt) REVERT: 5 469 MET cc_start: 0.7716 (mmt) cc_final: 0.7484 (mmm) REVERT: 5 497 MET cc_start: 0.6254 (mtm) cc_final: 0.5869 (mmm) REVERT: 5 530 TYR cc_start: 0.7992 (t80) cc_final: 0.7664 (t80) REVERT: 5 543 GLN cc_start: 0.4736 (pt0) cc_final: 0.4248 (pm20) REVERT: 5 675 ARG cc_start: 0.7416 (ptt90) cc_final: 0.7159 (mtt180) REVERT: 6 644 MET cc_start: 0.6684 (mtm) cc_final: 0.6181 (mmt) REVERT: 6 653 HIS cc_start: 0.7148 (t-90) cc_final: 0.6496 (t-170) REVERT: 6 679 LEU cc_start: 0.8900 (tt) cc_final: 0.8516 (tt) REVERT: 6 720 ASN cc_start: 0.9279 (t0) cc_final: 0.8904 (p0) REVERT: 2 236 GLU cc_start: 0.7750 (tp30) cc_final: 0.7003 (tp30) REVERT: 2 267 MET cc_start: 0.7843 (tpt) cc_final: 0.7408 (mmp) REVERT: 2 380 THR cc_start: 0.7142 (p) cc_final: 0.6840 (p) REVERT: 2 422 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7784 (tt0) REVERT: 2 622 GLU cc_start: 0.7901 (tp30) cc_final: 0.7504 (tp30) REVERT: 2 764 MET cc_start: 0.6740 (ptm) cc_final: 0.6433 (ppp) REVERT: 2 825 LEU cc_start: 0.8937 (mp) cc_final: 0.8278 (tt) REVERT: 7 112 HIS cc_start: 0.8287 (t-170) cc_final: 0.7881 (m-70) REVERT: 7 402 MET cc_start: 0.9504 (mmt) cc_final: 0.9280 (mmm) REVERT: 7 525 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8246 (pp20) REVERT: 7 711 ASP cc_start: 0.9315 (t0) cc_final: 0.9035 (p0) REVERT: C 19 LEU cc_start: 0.8930 (mt) cc_final: 0.8419 (mt) REVERT: C 38 ARG cc_start: 0.9168 (mtt90) cc_final: 0.8949 (mtt-85) REVERT: C 43 GLU cc_start: 0.8061 (tt0) cc_final: 0.7532 (tp30) REVERT: C 78 CYS cc_start: 0.9314 (t) cc_final: 0.9067 (m) REVERT: D 112 PHE cc_start: 0.6970 (m-80) cc_final: 0.6134 (m-10) REVERT: D 180 GLU cc_start: 0.8340 (pt0) cc_final: 0.7797 (pt0) REVERT: E 47 PRO cc_start: 0.8655 (Cg_exo) cc_final: 0.8434 (Cg_endo) REVERT: E 172 MET cc_start: 0.8672 (ptm) cc_final: 0.8218 (ppp) REVERT: F 132 GLU cc_start: 0.8260 (tm-30) cc_final: 0.8005 (tm-30) REVERT: F 143 TYR cc_start: 0.8379 (t80) cc_final: 0.7643 (t80) REVERT: F 183 HIS cc_start: 0.8443 (t70) cc_final: 0.8206 (t-170) REVERT: G 351 TRP cc_start: 0.5908 (p90) cc_final: 0.5491 (p-90) REVERT: G 378 LEU cc_start: 0.8901 (mt) cc_final: 0.8539 (tp) REVERT: G 476 ASN cc_start: 0.5432 (t0) cc_final: 0.5162 (t0) REVERT: G 497 GLN cc_start: 0.6283 (mt0) cc_final: 0.5310 (tm-30) REVERT: G 541 ASN cc_start: 0.8820 (t0) cc_final: 0.8469 (t0) REVERT: B 188 MET cc_start: 0.8108 (mtm) cc_final: 0.7825 (mpp) REVERT: B 424 LEU cc_start: 0.9493 (mt) cc_final: 0.9276 (tt) REVERT: B 483 PHE cc_start: 0.9245 (m-10) cc_final: 0.8900 (m-80) REVERT: B 650 ASP cc_start: 0.7170 (t0) cc_final: 0.6770 (t0) REVERT: A 1490 PHE cc_start: 0.8678 (t80) cc_final: 0.7817 (t80) REVERT: A 1497 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8504 (mm-30) REVERT: A 1498 PHE cc_start: 0.8197 (m-10) cc_final: 0.7881 (m-10) REVERT: A 1613 VAL cc_start: 0.8019 (t) cc_final: 0.7695 (p) REVERT: A 1688 TRP cc_start: 0.8001 (m-10) cc_final: 0.7732 (m-10) REVERT: A 1737 ASP cc_start: 0.8580 (m-30) cc_final: 0.8325 (p0) REVERT: A 1738 ASN cc_start: 0.8946 (m-40) cc_final: 0.8620 (m-40) REVERT: A 1905 TYR cc_start: 0.8735 (p90) cc_final: 0.8332 (p90) REVERT: A 1912 MET cc_start: 0.8853 (mmt) cc_final: 0.8401 (mmm) REVERT: A 2062 MET cc_start: 0.7480 (pmm) cc_final: 0.7131 (mpp) outliers start: 24 outliers final: 3 residues processed: 997 average time/residue: 0.4855 time to fit residues: 794.4369 Evaluate side-chains 492 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 489 time to evaluate : 4.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 507 optimal weight: 7.9990 chunk 455 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 307 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 471 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 350 optimal weight: 6.9990 chunk 545 optimal weight: 40.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 29 GLN 3 46 GLN 3 259 GLN 3 417 GLN 3 493 GLN 3 532 ASN ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 582 HIS 4 757 HIS ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 245 HIS ** 5 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 571 HIS 5 585 ASN ** 5 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 366 ASN 6 524 HIS 6 653 HIS 6 730 HIS 6 750 GLN 2 238 ASN 2 290 HIS 2 561 HIS 7 90 ASN 7 107 GLN 7 326 HIS 7 455 ASN 7 554 ASN 7 568 ASN 7 620 HIS C 33 HIS C 201 GLN D 167 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS F 160 GLN F 186 HIS G 70 HIS G 101 GLN G 138 GLN G 286 GLN G 342 ASN G 575 ASN G 624 ASN B 189 GLN B 505 GLN B 609 GLN B 628 HIS A1373 ASN A1413 ASN A1657 ASN A1703 ASN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1742 ASN ** A1838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 HIS A2196 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 48430 Z= 0.245 Angle : 0.837 12.688 65697 Z= 0.439 Chirality : 0.047 0.253 7680 Planarity : 0.006 0.103 8241 Dihedral : 11.562 151.898 6979 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.20 % Favored : 91.68 % Rotamer: Outliers : 0.16 % Allowed : 3.20 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.81 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.81 (0.10), residues: 5814 helix: -0.99 (0.10), residues: 2310 sheet: -2.01 (0.19), residues: 672 loop : -2.60 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1689 HIS 0.014 0.002 HIS A2178 PHE 0.041 0.002 PHE 7 93 TYR 0.039 0.002 TYR G 288 ARG 0.015 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 663 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8452 (t80) cc_final: 0.8222 (t80) REVERT: 3 105 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: 3 320 LEU cc_start: 0.9230 (pp) cc_final: 0.8913 (pp) REVERT: 3 382 LEU cc_start: 0.8046 (mp) cc_final: 0.7793 (tt) REVERT: 3 395 ASN cc_start: 0.8069 (p0) cc_final: 0.7606 (p0) REVERT: 3 471 CYS cc_start: 0.9309 (m) cc_final: 0.9108 (m) REVERT: 4 439 PHE cc_start: 0.8142 (t80) cc_final: 0.7764 (t80) REVERT: 4 535 ASP cc_start: 0.9013 (m-30) cc_final: 0.8735 (p0) REVERT: 4 637 MET cc_start: 0.8030 (mmt) cc_final: 0.7612 (mmm) REVERT: 4 749 MET cc_start: 0.9247 (mmp) cc_final: 0.8865 (mmm) REVERT: 5 68 LEU cc_start: 0.9125 (mt) cc_final: 0.8673 (tt) REVERT: 5 73 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7862 (pm20) REVERT: 5 138 ILE cc_start: 0.7106 (mt) cc_final: 0.6755 (pt) REVERT: 5 243 ILE cc_start: 0.9023 (mm) cc_final: 0.8391 (pt) REVERT: 5 254 GLN cc_start: 0.7237 (tp40) cc_final: 0.6989 (tp40) REVERT: 5 278 CYS cc_start: 0.3623 (m) cc_final: 0.3335 (m) REVERT: 5 291 ARG cc_start: 0.7194 (mtt-85) cc_final: 0.6101 (tmt-80) REVERT: 5 303 SER cc_start: 0.7829 (p) cc_final: 0.7611 (m) REVERT: 5 388 ILE cc_start: 0.7509 (mm) cc_final: 0.7194 (mm) REVERT: 5 478 CYS cc_start: 0.6689 (t) cc_final: 0.6379 (t) REVERT: 5 543 GLN cc_start: 0.4696 (pt0) cc_final: 0.4414 (pm20) REVERT: 5 599 MET cc_start: 0.7535 (tpt) cc_final: 0.7188 (tpt) REVERT: 5 675 ARG cc_start: 0.7393 (ptt90) cc_final: 0.7039 (mtt180) REVERT: 6 393 ASP cc_start: 0.6071 (t0) cc_final: 0.5837 (p0) REVERT: 6 549 LEU cc_start: 0.9358 (mt) cc_final: 0.9156 (mt) REVERT: 6 653 HIS cc_start: 0.6700 (t70) cc_final: 0.6499 (t-170) REVERT: 6 720 ASN cc_start: 0.9097 (t0) cc_final: 0.8845 (p0) REVERT: 2 267 MET cc_start: 0.8090 (tpt) cc_final: 0.7635 (mmp) REVERT: 2 633 LYS cc_start: 0.4499 (tptt) cc_final: 0.3959 (tptt) REVERT: 2 825 LEU cc_start: 0.8848 (mp) cc_final: 0.8343 (tt) REVERT: 7 211 CYS cc_start: 0.9055 (t) cc_final: 0.8493 (p) REVERT: 7 458 LEU cc_start: 0.8725 (mt) cc_final: 0.8513 (mt) REVERT: 7 498 MET cc_start: 0.6611 (ptt) cc_final: 0.6323 (ppp) REVERT: 7 711 ASP cc_start: 0.9305 (t0) cc_final: 0.8978 (p0) REVERT: C 38 ARG cc_start: 0.8968 (mtt90) cc_final: 0.8503 (mtt-85) REVERT: C 43 GLU cc_start: 0.8073 (tt0) cc_final: 0.7270 (tp30) REVERT: C 85 CYS cc_start: 0.8409 (m) cc_final: 0.8182 (m) REVERT: C 127 GLU cc_start: 0.7918 (pt0) cc_final: 0.7194 (pt0) REVERT: C 181 PHE cc_start: 0.5814 (m-10) cc_final: 0.5527 (m-10) REVERT: D 8 GLN cc_start: 0.7277 (pt0) cc_final: 0.5902 (mp10) REVERT: D 66 MET cc_start: 0.7947 (tpp) cc_final: 0.7740 (ppp) REVERT: D 118 ASN cc_start: 0.7503 (p0) cc_final: 0.7108 (m-40) REVERT: D 180 GLU cc_start: 0.8570 (pt0) cc_final: 0.7882 (tt0) REVERT: E 47 PRO cc_start: 0.8993 (Cg_exo) cc_final: 0.8772 (Cg_endo) REVERT: E 105 PHE cc_start: 0.8495 (m-80) cc_final: 0.8053 (m-10) REVERT: E 115 PHE cc_start: 0.8019 (t80) cc_final: 0.7813 (t80) REVERT: E 191 MET cc_start: 0.6528 (mmm) cc_final: 0.6117 (tpp) REVERT: F 183 HIS cc_start: 0.8458 (t70) cc_final: 0.8133 (t70) REVERT: G 366 MET cc_start: 0.9175 (mmm) cc_final: 0.8871 (mmm) REVERT: G 575 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8586 (t0) REVERT: B 182 SER cc_start: 0.8444 (t) cc_final: 0.8239 (p) REVERT: B 188 MET cc_start: 0.8185 (mtm) cc_final: 0.7874 (mpp) REVERT: B 355 THR cc_start: 0.9438 (m) cc_final: 0.9227 (p) REVERT: B 469 LEU cc_start: 0.9175 (tp) cc_final: 0.8954 (pp) REVERT: B 483 PHE cc_start: 0.9130 (m-10) cc_final: 0.8863 (m-10) REVERT: B 541 ILE cc_start: 0.8960 (mp) cc_final: 0.8753 (mp) REVERT: B 639 MET cc_start: 0.7756 (mtt) cc_final: 0.7439 (mtt) REVERT: B 641 LEU cc_start: 0.8994 (mm) cc_final: 0.8743 (mm) REVERT: A 1482 MET cc_start: 0.6790 (mpp) cc_final: 0.6344 (mmt) REVERT: A 1487 LEU cc_start: 0.9742 (tt) cc_final: 0.9493 (mm) REVERT: A 1490 PHE cc_start: 0.8682 (t80) cc_final: 0.7750 (t80) REVERT: A 1497 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8556 (mm-30) REVERT: A 1498 PHE cc_start: 0.8125 (m-10) cc_final: 0.7738 (m-10) REVERT: A 1597 ILE cc_start: 0.6899 (mp) cc_final: 0.6388 (mp) REVERT: A 1668 MET cc_start: 0.8806 (mmp) cc_final: 0.8360 (mmm) REVERT: A 1675 LEU cc_start: 0.9338 (tp) cc_final: 0.9124 (pp) REVERT: A 1688 TRP cc_start: 0.7674 (m-10) cc_final: 0.7385 (m-10) REVERT: A 1737 ASP cc_start: 0.8770 (m-30) cc_final: 0.8080 (p0) REVERT: A 1738 ASN cc_start: 0.8982 (m-40) cc_final: 0.8629 (m-40) REVERT: A 1838 ASN cc_start: 0.8879 (m110) cc_final: 0.8644 (m-40) REVERT: A 1905 TYR cc_start: 0.8682 (p90) cc_final: 0.8194 (p90) REVERT: A 1912 MET cc_start: 0.8556 (mmt) cc_final: 0.7887 (mmm) REVERT: A 2062 MET cc_start: 0.7986 (pmm) cc_final: 0.7081 (mpp) REVERT: A 2175 MET cc_start: 0.8778 (ttm) cc_final: 0.8564 (ttm) outliers start: 8 outliers final: 2 residues processed: 670 average time/residue: 0.4707 time to fit residues: 528.4890 Evaluate side-chains 462 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 458 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 303 optimal weight: 40.0000 chunk 169 optimal weight: 0.7980 chunk 454 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 546 optimal weight: 20.0000 chunk 590 optimal weight: 20.0000 chunk 486 optimal weight: 0.9990 chunk 542 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 438 optimal weight: 20.0000 overall best weight: 3.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 530 HIS ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 284 ASN 5 560 HIS 5 625 ASN ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 658 GLN 6 750 GLN 2 248 HIS 2 290 HIS 2 561 HIS ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS C 25 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN D 146 GLN D 167 HIS D 169 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1835 HIS ** A1837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 48430 Z= 0.253 Angle : 0.773 12.063 65697 Z= 0.404 Chirality : 0.046 0.249 7680 Planarity : 0.005 0.085 8241 Dihedral : 11.178 146.378 6979 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.27 % Favored : 91.62 % Rotamer: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.81 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.43 (0.10), residues: 5814 helix: -0.46 (0.10), residues: 2344 sheet: -1.91 (0.19), residues: 683 loop : -2.59 (0.11), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 434 HIS 0.014 0.001 HIS 3 175 PHE 0.034 0.002 PHE 5 31 TYR 0.035 0.002 TYR G 288 ARG 0.025 0.001 ARG 3 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 576 time to evaluate : 4.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8465 (t80) cc_final: 0.8214 (t80) REVERT: 3 382 LEU cc_start: 0.8036 (mp) cc_final: 0.7813 (tt) REVERT: 3 395 ASN cc_start: 0.7719 (p0) cc_final: 0.7335 (p0) REVERT: 4 233 MET cc_start: 0.8397 (ptt) cc_final: 0.7772 (ttt) REVERT: 4 382 MET cc_start: 0.8101 (tmm) cc_final: 0.7440 (tpp) REVERT: 4 439 PHE cc_start: 0.8296 (t80) cc_final: 0.7857 (t80) REVERT: 4 537 LYS cc_start: 0.9457 (mttm) cc_final: 0.9244 (mttt) REVERT: 4 637 MET cc_start: 0.8072 (mmt) cc_final: 0.7650 (mmm) REVERT: 4 749 MET cc_start: 0.9207 (mmp) cc_final: 0.8878 (mmm) REVERT: 4 801 MET cc_start: 0.8203 (mmm) cc_final: 0.7918 (mmm) REVERT: 5 73 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7738 (pm20) REVERT: 5 138 ILE cc_start: 0.7298 (mt) cc_final: 0.6722 (pt) REVERT: 5 277 THR cc_start: 0.6131 (m) cc_final: 0.5862 (m) REVERT: 5 291 ARG cc_start: 0.7220 (mtt-85) cc_final: 0.6080 (tmt-80) REVERT: 5 303 SER cc_start: 0.7937 (p) cc_final: 0.7700 (m) REVERT: 5 388 ILE cc_start: 0.7609 (mm) cc_final: 0.7292 (mm) REVERT: 5 393 MET cc_start: 0.4978 (mmm) cc_final: 0.4703 (mmm) REVERT: 5 478 CYS cc_start: 0.6757 (t) cc_final: 0.6319 (t) REVERT: 5 485 MET cc_start: 0.7284 (ttt) cc_final: 0.7013 (mmm) REVERT: 5 587 GLN cc_start: 0.7171 (tt0) cc_final: 0.6623 (mm-40) REVERT: 5 599 MET cc_start: 0.7550 (tpt) cc_final: 0.7022 (tpt) REVERT: 5 675 ARG cc_start: 0.7492 (ptt90) cc_final: 0.7181 (mtt-85) REVERT: 5 690 ASP cc_start: 0.8763 (m-30) cc_final: 0.8108 (t0) REVERT: 6 720 ASN cc_start: 0.9235 (t0) cc_final: 0.8868 (p0) REVERT: 2 267 MET cc_start: 0.8209 (tpt) cc_final: 0.7707 (mmp) REVERT: 2 335 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8288 (ttpp) REVERT: 2 633 LYS cc_start: 0.3879 (tptt) cc_final: 0.3459 (tptt) REVERT: 2 658 ASN cc_start: 0.8964 (p0) cc_final: 0.8675 (p0) REVERT: 2 764 MET cc_start: 0.5416 (ppp) cc_final: 0.4391 (mtt) REVERT: 2 825 LEU cc_start: 0.9019 (mp) cc_final: 0.8397 (tt) REVERT: 7 125 MET cc_start: 0.7634 (mmp) cc_final: 0.7406 (mmm) REVERT: 7 211 CYS cc_start: 0.9020 (t) cc_final: 0.8479 (p) REVERT: 7 402 MET cc_start: 0.9376 (mmp) cc_final: 0.9151 (mmm) REVERT: 7 711 ASP cc_start: 0.9278 (t0) cc_final: 0.8966 (p0) REVERT: C 38 ARG cc_start: 0.8995 (mtt90) cc_final: 0.8611 (mtt-85) REVERT: C 43 GLU cc_start: 0.8042 (tt0) cc_final: 0.7216 (tp30) REVERT: C 77 LEU cc_start: 0.8901 (mt) cc_final: 0.8700 (mt) REVERT: C 181 PHE cc_start: 0.6078 (m-10) cc_final: 0.5764 (m-10) REVERT: D 8 GLN cc_start: 0.7193 (pt0) cc_final: 0.5908 (mp10) REVERT: D 112 PHE cc_start: 0.7290 (m-80) cc_final: 0.6302 (m-10) REVERT: D 118 ASN cc_start: 0.7394 (p0) cc_final: 0.7062 (m-40) REVERT: D 180 GLU cc_start: 0.8576 (pt0) cc_final: 0.7718 (tt0) REVERT: E 169 LEU cc_start: 0.8378 (mp) cc_final: 0.7960 (mp) REVERT: E 172 MET cc_start: 0.8818 (ptm) cc_final: 0.8568 (ptm) REVERT: E 186 ASP cc_start: 0.9081 (p0) cc_final: 0.8869 (p0) REVERT: F 132 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7658 (tm-30) REVERT: F 183 HIS cc_start: 0.8395 (t70) cc_final: 0.8119 (t70) REVERT: G 14 LYS cc_start: 0.9533 (ttpt) cc_final: 0.9277 (tptt) REVERT: G 45 LEU cc_start: 0.8867 (mt) cc_final: 0.8602 (mt) REVERT: G 366 MET cc_start: 0.9181 (mmm) cc_final: 0.8948 (mmm) REVERT: G 391 ILE cc_start: 0.8771 (tp) cc_final: 0.8503 (tp) REVERT: G 423 GLU cc_start: 0.8556 (mp0) cc_final: 0.8319 (mp0) REVERT: G 541 ASN cc_start: 0.8878 (t0) cc_final: 0.8653 (t0) REVERT: G 575 ASN cc_start: 0.8962 (t0) cc_final: 0.8738 (t0) REVERT: B 182 SER cc_start: 0.8445 (t) cc_final: 0.8215 (p) REVERT: B 188 MET cc_start: 0.8643 (mtm) cc_final: 0.8172 (mpp) REVERT: B 230 MET cc_start: 0.6171 (tmm) cc_final: 0.5886 (tpp) REVERT: B 432 LEU cc_start: 0.9357 (tp) cc_final: 0.9152 (tt) REVERT: B 465 LEU cc_start: 0.8715 (tp) cc_final: 0.8415 (pp) REVERT: B 483 PHE cc_start: 0.9285 (m-10) cc_final: 0.8908 (m-10) REVERT: B 541 ILE cc_start: 0.9084 (mp) cc_final: 0.8859 (mp) REVERT: B 673 MET cc_start: 0.8404 (tpp) cc_final: 0.7582 (tpp) REVERT: A 1482 MET cc_start: 0.6829 (mpp) cc_final: 0.6348 (mmt) REVERT: A 1490 PHE cc_start: 0.8636 (t80) cc_final: 0.7892 (t80) REVERT: A 1497 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8600 (mm-30) REVERT: A 1498 PHE cc_start: 0.7997 (m-10) cc_final: 0.7717 (m-10) REVERT: A 1649 LEU cc_start: 0.9342 (mm) cc_final: 0.9060 (pp) REVERT: A 1668 MET cc_start: 0.8762 (mmp) cc_final: 0.8480 (mmm) REVERT: A 1737 ASP cc_start: 0.8616 (m-30) cc_final: 0.7896 (p0) REVERT: A 1738 ASN cc_start: 0.9025 (m-40) cc_final: 0.8625 (m-40) REVERT: A 1812 LEU cc_start: 0.9389 (tp) cc_final: 0.9132 (tp) REVERT: A 1905 TYR cc_start: 0.8640 (p90) cc_final: 0.8199 (p90) REVERT: A 1912 MET cc_start: 0.8484 (mmt) cc_final: 0.7843 (mmm) REVERT: A 2056 LYS cc_start: 0.8980 (mptt) cc_final: 0.8658 (mmtt) REVERT: A 2062 MET cc_start: 0.8080 (pmm) cc_final: 0.7270 (mpp) outliers start: 3 outliers final: 2 residues processed: 578 average time/residue: 0.4665 time to fit residues: 456.0244 Evaluate side-chains 441 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 439 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 540 optimal weight: 50.0000 chunk 411 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 60 optimal weight: 40.0000 chunk 260 optimal weight: 4.9990 chunk 367 optimal weight: 0.4980 chunk 548 optimal weight: 8.9990 chunk 580 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 520 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 175 HIS ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 530 HIS 3 531 GLN ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 354 HIS ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 284 ASN 5 424 GLN 5 576 HIS 5 625 ASN 5 685 GLN ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 653 HIS 6 698 ASN 6 750 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 531 HIS ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS 7 622 HIS C 33 HIS D 167 HIS E 138 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 48430 Z= 0.222 Angle : 0.731 12.231 65697 Z= 0.382 Chirality : 0.045 0.243 7680 Planarity : 0.005 0.062 8241 Dihedral : 10.896 146.935 6979 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.05 % Favored : 91.85 % Rotamer: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.81 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.17 (0.11), residues: 5814 helix: -0.19 (0.10), residues: 2347 sheet: -1.76 (0.19), residues: 687 loop : -2.51 (0.11), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1689 HIS 0.009 0.001 HIS A2168 PHE 0.029 0.002 PHE 5 31 TYR 0.036 0.002 TYR G 288 ARG 0.013 0.001 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 556 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8468 (t80) cc_final: 0.8194 (t80) REVERT: 3 382 LEU cc_start: 0.8007 (mp) cc_final: 0.7767 (tt) REVERT: 3 395 ASN cc_start: 0.7699 (p0) cc_final: 0.7330 (p0) REVERT: 4 233 MET cc_start: 0.8756 (ptt) cc_final: 0.8438 (ppp) REVERT: 4 382 MET cc_start: 0.8412 (tmm) cc_final: 0.7759 (tpp) REVERT: 4 439 PHE cc_start: 0.8332 (t80) cc_final: 0.7875 (t80) REVERT: 4 637 MET cc_start: 0.8112 (mmt) cc_final: 0.7670 (mmm) REVERT: 4 749 MET cc_start: 0.9087 (mmp) cc_final: 0.8752 (mmm) REVERT: 4 801 MET cc_start: 0.8504 (mmm) cc_final: 0.8150 (mmm) REVERT: 5 68 LEU cc_start: 0.9014 (mt) cc_final: 0.8567 (tt) REVERT: 5 73 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7856 (pm20) REVERT: 5 263 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8282 (tt0) REVERT: 5 291 ARG cc_start: 0.7189 (mtt-85) cc_final: 0.5747 (tmt-80) REVERT: 5 388 ILE cc_start: 0.7632 (mm) cc_final: 0.7343 (mm) REVERT: 5 393 MET cc_start: 0.5059 (mmm) cc_final: 0.4813 (mmm) REVERT: 5 478 CYS cc_start: 0.6388 (t) cc_final: 0.5967 (t) REVERT: 5 485 MET cc_start: 0.7305 (ttt) cc_final: 0.7067 (mmm) REVERT: 5 599 MET cc_start: 0.7155 (tpt) cc_final: 0.6494 (tpt) REVERT: 5 675 ARG cc_start: 0.7574 (ptt90) cc_final: 0.7159 (mtt180) REVERT: 6 644 MET cc_start: 0.6710 (mtm) cc_final: 0.6294 (mmt) REVERT: 6 653 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.5908 (t70) REVERT: 6 657 GLU cc_start: 0.7480 (pt0) cc_final: 0.6772 (pt0) REVERT: 6 679 LEU cc_start: 0.8801 (tp) cc_final: 0.8323 (tp) REVERT: 6 720 ASN cc_start: 0.9263 (t0) cc_final: 0.8877 (p0) REVERT: 2 267 MET cc_start: 0.8145 (tpt) cc_final: 0.7673 (mmp) REVERT: 2 633 LYS cc_start: 0.4074 (tptt) cc_final: 0.3850 (tptt) REVERT: 2 658 ASN cc_start: 0.9000 (p0) cc_final: 0.8780 (p0) REVERT: 7 125 MET cc_start: 0.7798 (mmp) cc_final: 0.7573 (mmm) REVERT: 7 211 CYS cc_start: 0.9049 (t) cc_final: 0.8468 (p) REVERT: 7 711 ASP cc_start: 0.9312 (t0) cc_final: 0.9011 (p0) REVERT: C 38 ARG cc_start: 0.8955 (mtt90) cc_final: 0.8458 (mtt-85) REVERT: C 43 GLU cc_start: 0.7884 (tt0) cc_final: 0.7257 (tp30) REVERT: C 62 MET cc_start: 0.6687 (pmm) cc_final: 0.6244 (pmm) REVERT: C 127 GLU cc_start: 0.7582 (pt0) cc_final: 0.6842 (pt0) REVERT: D 8 GLN cc_start: 0.7419 (pt0) cc_final: 0.6311 (mp10) REVERT: D 118 ASN cc_start: 0.7253 (p0) cc_final: 0.6807 (m-40) REVERT: D 180 GLU cc_start: 0.8610 (pt0) cc_final: 0.7922 (tt0) REVERT: E 20 PHE cc_start: 0.8674 (p90) cc_final: 0.8201 (p90) REVERT: E 173 GLU cc_start: 0.9111 (mp0) cc_final: 0.8758 (mp0) REVERT: F 183 HIS cc_start: 0.8384 (t70) cc_final: 0.8143 (t70) REVERT: G 45 LEU cc_start: 0.8886 (mt) cc_final: 0.8616 (mt) REVERT: G 366 MET cc_start: 0.8988 (mmm) cc_final: 0.8669 (mmm) REVERT: G 391 ILE cc_start: 0.8701 (tp) cc_final: 0.8332 (tp) REVERT: G 423 GLU cc_start: 0.8469 (mp0) cc_final: 0.8257 (mp0) REVERT: G 575 ASN cc_start: 0.8925 (t0) cc_final: 0.8701 (t0) REVERT: B 188 MET cc_start: 0.8495 (mtm) cc_final: 0.8149 (mpp) REVERT: B 230 MET cc_start: 0.6606 (tmm) cc_final: 0.6358 (tpp) REVERT: B 465 LEU cc_start: 0.8749 (tp) cc_final: 0.8525 (pp) REVERT: B 483 PHE cc_start: 0.9351 (m-10) cc_final: 0.9080 (m-10) REVERT: B 641 LEU cc_start: 0.8968 (mm) cc_final: 0.8722 (mm) REVERT: A 1482 MET cc_start: 0.6865 (mpp) cc_final: 0.6385 (mmt) REVERT: A 1490 PHE cc_start: 0.8558 (t80) cc_final: 0.7799 (t80) REVERT: A 1497 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8614 (mm-30) REVERT: A 1498 PHE cc_start: 0.8010 (m-10) cc_final: 0.7461 (m-10) REVERT: A 1597 ILE cc_start: 0.6797 (mp) cc_final: 0.6586 (mp) REVERT: A 1668 MET cc_start: 0.8833 (mmp) cc_final: 0.8605 (mmm) REVERT: A 1737 ASP cc_start: 0.8728 (m-30) cc_final: 0.8031 (p0) REVERT: A 1738 ASN cc_start: 0.9021 (m-40) cc_final: 0.8571 (m-40) REVERT: A 1827 LEU cc_start: 0.8394 (mm) cc_final: 0.8101 (mm) REVERT: A 1838 ASN cc_start: 0.8981 (m-40) cc_final: 0.8777 (m-40) REVERT: A 1894 MET cc_start: 0.6992 (ttm) cc_final: 0.6634 (ttp) REVERT: A 1905 TYR cc_start: 0.8730 (p90) cc_final: 0.8289 (p90) REVERT: A 1912 MET cc_start: 0.8457 (mmt) cc_final: 0.7916 (mmm) REVERT: A 2056 LYS cc_start: 0.9106 (mptt) cc_final: 0.8806 (mmtt) outliers start: 3 outliers final: 0 residues processed: 558 average time/residue: 0.4535 time to fit residues: 435.0649 Evaluate side-chains 429 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 428 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 483 optimal weight: 0.1980 chunk 329 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 432 optimal weight: 0.0020 chunk 239 optimal weight: 3.9990 chunk 495 optimal weight: 8.9990 chunk 401 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 521 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 424 GLN 5 576 HIS 5 625 ASN ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS F 94 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN A1654 GLN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 48430 Z= 0.189 Angle : 0.689 11.774 65697 Z= 0.358 Chirality : 0.044 0.203 7680 Planarity : 0.004 0.076 8241 Dihedral : 10.644 146.343 6979 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.98 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.90 (0.11), residues: 5814 helix: 0.10 (0.11), residues: 2351 sheet: -1.72 (0.19), residues: 728 loop : -2.40 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A1798 HIS 0.007 0.001 HIS 3 175 PHE 0.039 0.002 PHE B 458 TYR 0.036 0.001 TYR G 288 ARG 0.012 0.000 ARG 3 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 555 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8473 (t80) cc_final: 0.8183 (t80) REVERT: 3 395 ASN cc_start: 0.7666 (p0) cc_final: 0.7310 (p0) REVERT: 3 471 CYS cc_start: 0.9361 (m) cc_final: 0.9146 (m) REVERT: 4 233 MET cc_start: 0.9009 (ptt) cc_final: 0.8679 (ppp) REVERT: 4 314 MET cc_start: 0.7619 (tpt) cc_final: 0.6747 (mmm) REVERT: 4 382 MET cc_start: 0.8249 (tmm) cc_final: 0.7670 (tpp) REVERT: 4 439 PHE cc_start: 0.8397 (t80) cc_final: 0.7942 (t80) REVERT: 4 637 MET cc_start: 0.8088 (mmt) cc_final: 0.7663 (mmm) REVERT: 4 749 MET cc_start: 0.9089 (mmp) cc_final: 0.8699 (mmm) REVERT: 4 801 MET cc_start: 0.8500 (mmm) cc_final: 0.8113 (mmm) REVERT: 5 73 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7757 (pm20) REVERT: 5 138 ILE cc_start: 0.7532 (mt) cc_final: 0.7276 (mt) REVERT: 5 280 ARG cc_start: 0.6242 (pmt170) cc_final: 0.5844 (mtm180) REVERT: 5 291 ARG cc_start: 0.6972 (mtt-85) cc_final: 0.5845 (tmt-80) REVERT: 5 388 ILE cc_start: 0.7602 (mm) cc_final: 0.7313 (mm) REVERT: 5 393 MET cc_start: 0.5068 (mmm) cc_final: 0.4755 (mmm) REVERT: 5 478 CYS cc_start: 0.6371 (t) cc_final: 0.6012 (t) REVERT: 5 599 MET cc_start: 0.7282 (tpt) cc_final: 0.6642 (tpt) REVERT: 5 675 ARG cc_start: 0.7630 (ptt90) cc_final: 0.7120 (mtt180) REVERT: 5 690 ASP cc_start: 0.8641 (m-30) cc_final: 0.8039 (t0) REVERT: 6 679 LEU cc_start: 0.8615 (tp) cc_final: 0.8155 (tp) REVERT: 6 720 ASN cc_start: 0.9330 (t0) cc_final: 0.8980 (p0) REVERT: 2 267 MET cc_start: 0.8154 (tpt) cc_final: 0.7706 (mmp) REVERT: 2 658 ASN cc_start: 0.8984 (p0) cc_final: 0.8776 (p0) REVERT: 2 825 LEU cc_start: 0.9018 (mp) cc_final: 0.8673 (tt) REVERT: 7 211 CYS cc_start: 0.8988 (t) cc_final: 0.8733 (m) REVERT: 7 402 MET cc_start: 0.9379 (mmp) cc_final: 0.9059 (mmm) REVERT: 7 675 MET cc_start: 0.6835 (mmm) cc_final: 0.6440 (mmm) REVERT: 7 711 ASP cc_start: 0.9298 (t0) cc_final: 0.9005 (p0) REVERT: C 38 ARG cc_start: 0.8968 (mtt90) cc_final: 0.8458 (mtt-85) REVERT: C 43 GLU cc_start: 0.7849 (tt0) cc_final: 0.7225 (tp30) REVERT: C 62 MET cc_start: 0.6669 (pmm) cc_final: 0.6421 (pmm) REVERT: C 77 LEU cc_start: 0.8833 (mt) cc_final: 0.8625 (mt) REVERT: C 127 GLU cc_start: 0.7591 (pt0) cc_final: 0.6917 (pt0) REVERT: D 8 GLN cc_start: 0.7283 (pt0) cc_final: 0.6292 (mp10) REVERT: D 118 ASN cc_start: 0.7278 (p0) cc_final: 0.6763 (m-40) REVERT: D 180 GLU cc_start: 0.8503 (pt0) cc_final: 0.7877 (tt0) REVERT: E 20 PHE cc_start: 0.8735 (p90) cc_final: 0.8085 (p90) REVERT: E 113 MET cc_start: 0.7255 (mmp) cc_final: 0.6925 (mmp) REVERT: E 173 GLU cc_start: 0.9298 (mp0) cc_final: 0.8896 (mp0) REVERT: F 129 MET cc_start: 0.8841 (mmt) cc_final: 0.8519 (mmt) REVERT: F 183 HIS cc_start: 0.8344 (t70) cc_final: 0.8135 (t70) REVERT: G 45 LEU cc_start: 0.8916 (mt) cc_final: 0.8688 (mt) REVERT: G 391 ILE cc_start: 0.8738 (tp) cc_final: 0.8420 (tp) REVERT: G 575 ASN cc_start: 0.8927 (t0) cc_final: 0.8719 (t0) REVERT: B 188 MET cc_start: 0.8635 (mtm) cc_final: 0.8226 (mpp) REVERT: B 344 MET cc_start: 0.7076 (ptt) cc_final: 0.6709 (ptt) REVERT: B 465 LEU cc_start: 0.8785 (tp) cc_final: 0.8489 (pp) REVERT: B 483 PHE cc_start: 0.9265 (m-10) cc_final: 0.9029 (m-10) REVERT: B 673 MET cc_start: 0.8972 (tpp) cc_final: 0.7465 (tpp) REVERT: A 1482 MET cc_start: 0.7017 (mpp) cc_final: 0.6516 (mmt) REVERT: A 1490 PHE cc_start: 0.8489 (t80) cc_final: 0.7939 (t80) REVERT: A 1497 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8757 (mm-30) REVERT: A 1498 PHE cc_start: 0.8013 (m-10) cc_final: 0.7531 (m-10) REVERT: A 1649 LEU cc_start: 0.9314 (mm) cc_final: 0.9013 (pp) REVERT: A 1668 MET cc_start: 0.8940 (mmp) cc_final: 0.8645 (mmm) REVERT: A 1737 ASP cc_start: 0.8688 (m-30) cc_final: 0.7956 (p0) REVERT: A 1738 ASN cc_start: 0.9035 (m-40) cc_final: 0.8568 (m-40) REVERT: A 1798 TRP cc_start: 0.8231 (m-90) cc_final: 0.7655 (m-90) REVERT: A 1894 MET cc_start: 0.6825 (ttm) cc_final: 0.6615 (ttp) REVERT: A 1897 TYR cc_start: 0.3489 (m-80) cc_final: 0.3206 (m-80) REVERT: A 1905 TYR cc_start: 0.8759 (p90) cc_final: 0.8379 (p90) REVERT: A 1912 MET cc_start: 0.8407 (mmt) cc_final: 0.7878 (mmm) outliers start: 0 outliers final: 0 residues processed: 555 average time/residue: 0.4871 time to fit residues: 467.8214 Evaluate side-chains 424 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 195 optimal weight: 4.9990 chunk 523 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 581 optimal weight: 50.0000 chunk 482 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 305 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 175 HIS ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 185 ASN 5 576 HIS 5 625 ASN ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 ASN ** G 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2145 HIS A2196 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 48430 Z= 0.238 Angle : 0.723 11.406 65697 Z= 0.376 Chirality : 0.045 0.237 7680 Planarity : 0.005 0.072 8241 Dihedral : 10.637 144.954 6979 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.48 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.87 (0.11), residues: 5814 helix: 0.12 (0.11), residues: 2365 sheet: -1.64 (0.19), residues: 724 loop : -2.41 (0.11), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1798 HIS 0.012 0.001 HIS A2145 PHE 0.036 0.002 PHE B 458 TYR 0.035 0.002 TYR G 288 ARG 0.010 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8514 (t80) cc_final: 0.8178 (t80) REVERT: 3 395 ASN cc_start: 0.7589 (p0) cc_final: 0.7188 (p0) REVERT: 3 471 CYS cc_start: 0.9344 (m) cc_final: 0.9013 (m) REVERT: 4 233 MET cc_start: 0.8874 (ptt) cc_final: 0.7933 (mtt) REVERT: 4 314 MET cc_start: 0.7500 (tpt) cc_final: 0.6838 (mmm) REVERT: 4 382 MET cc_start: 0.8318 (tmm) cc_final: 0.7756 (tpp) REVERT: 4 439 PHE cc_start: 0.8351 (t80) cc_final: 0.7962 (t80) REVERT: 4 637 MET cc_start: 0.8185 (mmt) cc_final: 0.7675 (mmm) REVERT: 4 749 MET cc_start: 0.9029 (mmp) cc_final: 0.8621 (mmm) REVERT: 5 68 LEU cc_start: 0.9050 (mt) cc_final: 0.8595 (tt) REVERT: 5 73 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7738 (pm20) REVERT: 5 138 ILE cc_start: 0.7986 (mt) cc_final: 0.7335 (pt) REVERT: 5 291 ARG cc_start: 0.7088 (mtt-85) cc_final: 0.5895 (tmt-80) REVERT: 5 388 ILE cc_start: 0.7775 (mm) cc_final: 0.7514 (mm) REVERT: 5 478 CYS cc_start: 0.6632 (t) cc_final: 0.6155 (t) REVERT: 5 599 MET cc_start: 0.7271 (tpt) cc_final: 0.6568 (tpt) REVERT: 5 661 GLU cc_start: 0.9302 (mp0) cc_final: 0.8994 (pt0) REVERT: 5 675 ARG cc_start: 0.7780 (ptt90) cc_final: 0.7054 (mtt-85) REVERT: 5 690 ASP cc_start: 0.8663 (m-30) cc_final: 0.8084 (t0) REVERT: 6 679 LEU cc_start: 0.8480 (tp) cc_final: 0.8060 (tp) REVERT: 6 720 ASN cc_start: 0.9357 (t0) cc_final: 0.8999 (p0) REVERT: 2 267 MET cc_start: 0.8006 (tpt) cc_final: 0.7477 (mmp) REVERT: 2 658 ASN cc_start: 0.9000 (p0) cc_final: 0.8786 (p0) REVERT: 2 825 LEU cc_start: 0.9119 (mp) cc_final: 0.8786 (tt) REVERT: 7 211 CYS cc_start: 0.8885 (t) cc_final: 0.8676 (m) REVERT: 7 402 MET cc_start: 0.9371 (mmp) cc_final: 0.9059 (mmm) REVERT: 7 711 ASP cc_start: 0.9303 (t0) cc_final: 0.9011 (p0) REVERT: C 38 ARG cc_start: 0.8938 (mtt90) cc_final: 0.8472 (mtt-85) REVERT: C 43 GLU cc_start: 0.7884 (tt0) cc_final: 0.7222 (tp30) REVERT: C 77 LEU cc_start: 0.8810 (mt) cc_final: 0.8593 (mt) REVERT: D 8 GLN cc_start: 0.7320 (pt0) cc_final: 0.6716 (mp10) REVERT: D 180 GLU cc_start: 0.8703 (pt0) cc_final: 0.8241 (tt0) REVERT: D 188 ILE cc_start: 0.9370 (mt) cc_final: 0.9004 (tp) REVERT: E 20 PHE cc_start: 0.8821 (p90) cc_final: 0.8153 (p90) REVERT: E 113 MET cc_start: 0.7511 (mmp) cc_final: 0.7140 (mmp) REVERT: G 391 ILE cc_start: 0.8512 (tp) cc_final: 0.8147 (tp) REVERT: G 575 ASN cc_start: 0.8958 (t0) cc_final: 0.8721 (t0) REVERT: B 344 MET cc_start: 0.7016 (ptt) cc_final: 0.6768 (ptt) REVERT: B 465 LEU cc_start: 0.8753 (tp) cc_final: 0.8428 (pp) REVERT: B 483 PHE cc_start: 0.9307 (m-10) cc_final: 0.8937 (m-10) REVERT: B 639 MET cc_start: 0.8586 (mmp) cc_final: 0.7600 (mmp) REVERT: B 673 MET cc_start: 0.9024 (tpp) cc_final: 0.7525 (tpp) REVERT: A 1482 MET cc_start: 0.6408 (mpp) cc_final: 0.5959 (mmt) REVERT: A 1490 PHE cc_start: 0.8536 (t80) cc_final: 0.7982 (t80) REVERT: A 1497 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8778 (mm-30) REVERT: A 1498 PHE cc_start: 0.8063 (m-10) cc_final: 0.7546 (m-10) REVERT: A 1668 MET cc_start: 0.8996 (mmp) cc_final: 0.8656 (mmm) REVERT: A 1737 ASP cc_start: 0.8749 (m-30) cc_final: 0.8044 (p0) REVERT: A 1738 ASN cc_start: 0.9003 (m-40) cc_final: 0.8504 (m-40) REVERT: A 1796 LYS cc_start: 0.8181 (pttm) cc_final: 0.7771 (mptt) REVERT: A 1827 LEU cc_start: 0.8373 (mm) cc_final: 0.8110 (mm) REVERT: A 1845 LEU cc_start: 0.9381 (mm) cc_final: 0.8934 (pp) REVERT: A 1894 MET cc_start: 0.7011 (ttm) cc_final: 0.6771 (ttp) REVERT: A 1905 TYR cc_start: 0.8698 (p90) cc_final: 0.8390 (p90) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.4441 time to fit residues: 406.3996 Evaluate side-chains 408 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 560 optimal weight: 1.9990 chunk 65 optimal weight: 50.0000 chunk 331 optimal weight: 0.8980 chunk 424 optimal weight: 0.0370 chunk 329 optimal weight: 6.9990 chunk 489 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 579 optimal weight: 9.9990 chunk 362 optimal weight: 20.0000 chunk 353 optimal weight: 0.0870 chunk 267 optimal weight: 6.9990 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 569 HIS ** 4 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS 5 625 ASN ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 556 HIS 6 750 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS C 82 ASN D 8 GLN D 128 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN A2143 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 48430 Z= 0.168 Angle : 0.682 11.129 65697 Z= 0.349 Chirality : 0.044 0.272 7680 Planarity : 0.004 0.077 8241 Dihedral : 10.479 145.656 6979 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.65 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.65 (0.11), residues: 5814 helix: 0.34 (0.11), residues: 2374 sheet: -1.47 (0.19), residues: 723 loop : -2.35 (0.11), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1798 HIS 0.009 0.001 HIS 5 676 PHE 0.032 0.001 PHE B 458 TYR 0.037 0.001 TYR G 288 ARG 0.013 0.000 ARG F 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 4.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8459 (t80) cc_final: 0.8117 (t80) REVERT: 3 129 LEU cc_start: 0.8454 (tt) cc_final: 0.8242 (mt) REVERT: 3 282 LEU cc_start: 0.9018 (mm) cc_final: 0.8779 (mm) REVERT: 3 395 ASN cc_start: 0.7549 (p0) cc_final: 0.7149 (p0) REVERT: 3 471 CYS cc_start: 0.9237 (m) cc_final: 0.9024 (m) REVERT: 4 233 MET cc_start: 0.8883 (ptt) cc_final: 0.8664 (ppp) REVERT: 4 280 MET cc_start: 0.4752 (mmm) cc_final: 0.4509 (mmm) REVERT: 4 314 MET cc_start: 0.7747 (tpt) cc_final: 0.7024 (mmm) REVERT: 4 382 MET cc_start: 0.8275 (tmm) cc_final: 0.7940 (tpp) REVERT: 4 439 PHE cc_start: 0.8410 (t80) cc_final: 0.8048 (t80) REVERT: 4 565 LEU cc_start: 0.8805 (tt) cc_final: 0.8475 (tt) REVERT: 4 566 LEU cc_start: 0.8911 (tp) cc_final: 0.8191 (pt) REVERT: 4 637 MET cc_start: 0.8060 (mmt) cc_final: 0.7573 (mmm) REVERT: 4 749 MET cc_start: 0.8959 (mmp) cc_final: 0.8561 (mmm) REVERT: 5 68 LEU cc_start: 0.8943 (mt) cc_final: 0.8469 (tt) REVERT: 5 73 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7675 (pm20) REVERT: 5 138 ILE cc_start: 0.7437 (mt) cc_final: 0.7181 (mm) REVERT: 5 291 ARG cc_start: 0.7076 (mtt-85) cc_final: 0.5847 (tmt-80) REVERT: 5 388 ILE cc_start: 0.7541 (mm) cc_final: 0.7207 (mm) REVERT: 5 478 CYS cc_start: 0.6580 (t) cc_final: 0.6011 (t) REVERT: 5 599 MET cc_start: 0.7434 (tpt) cc_final: 0.6804 (tpt) REVERT: 5 690 ASP cc_start: 0.8506 (m-30) cc_final: 0.8037 (t0) REVERT: 6 679 LEU cc_start: 0.8417 (tp) cc_final: 0.8005 (tp) REVERT: 6 720 ASN cc_start: 0.9291 (t0) cc_final: 0.8934 (p0) REVERT: 2 267 MET cc_start: 0.7904 (tpt) cc_final: 0.7391 (mmp) REVERT: 2 527 VAL cc_start: 0.6244 (t) cc_final: 0.6027 (t) REVERT: 2 658 ASN cc_start: 0.8910 (p0) cc_final: 0.8672 (p0) REVERT: 2 792 ASP cc_start: 0.9026 (m-30) cc_final: 0.7770 (t70) REVERT: 2 825 LEU cc_start: 0.8992 (mp) cc_final: 0.8746 (tt) REVERT: 7 125 MET cc_start: 0.8142 (mmp) cc_final: 0.7831 (mmm) REVERT: 7 211 CYS cc_start: 0.8808 (t) cc_final: 0.8590 (m) REVERT: 7 402 MET cc_start: 0.9366 (mmp) cc_final: 0.9050 (mmm) REVERT: 7 675 MET cc_start: 0.6631 (mmm) cc_final: 0.6244 (mmm) REVERT: 7 711 ASP cc_start: 0.9312 (t0) cc_final: 0.9035 (p0) REVERT: C 38 ARG cc_start: 0.8867 (mtt90) cc_final: 0.8356 (mtm-85) REVERT: C 43 GLU cc_start: 0.7966 (tt0) cc_final: 0.7135 (tp30) REVERT: D 8 GLN cc_start: 0.7480 (pt0) cc_final: 0.6342 (mp10) REVERT: D 118 ASN cc_start: 0.7706 (p0) cc_final: 0.7301 (m-40) REVERT: D 180 GLU cc_start: 0.8575 (pt0) cc_final: 0.8223 (tt0) REVERT: D 188 ILE cc_start: 0.9453 (mt) cc_final: 0.9055 (tp) REVERT: E 20 PHE cc_start: 0.8759 (p90) cc_final: 0.8170 (p90) REVERT: F 72 CYS cc_start: 0.8188 (t) cc_final: 0.7883 (t) REVERT: F 132 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7328 (tm-30) REVERT: F 202 MET cc_start: 0.7858 (mmm) cc_final: 0.7508 (tpp) REVERT: G 575 ASN cc_start: 0.8931 (t0) cc_final: 0.8697 (t0) REVERT: B 344 MET cc_start: 0.7277 (ptt) cc_final: 0.6902 (ptt) REVERT: B 465 LEU cc_start: 0.8777 (tp) cc_final: 0.8457 (pp) REVERT: B 483 PHE cc_start: 0.9237 (m-10) cc_final: 0.8863 (m-10) REVERT: B 639 MET cc_start: 0.8266 (mmp) cc_final: 0.7442 (mmp) REVERT: B 673 MET cc_start: 0.9095 (tpp) cc_final: 0.7530 (tpp) REVERT: A 1482 MET cc_start: 0.6520 (mpp) cc_final: 0.6040 (mmt) REVERT: A 1486 TYR cc_start: 0.8478 (t80) cc_final: 0.8122 (t80) REVERT: A 1490 PHE cc_start: 0.8478 (t80) cc_final: 0.7926 (t80) REVERT: A 1497 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8764 (mm-30) REVERT: A 1498 PHE cc_start: 0.8005 (m-10) cc_final: 0.7572 (m-10) REVERT: A 1649 LEU cc_start: 0.9329 (mm) cc_final: 0.9010 (pp) REVERT: A 1668 MET cc_start: 0.8954 (mmp) cc_final: 0.8570 (mmm) REVERT: A 1737 ASP cc_start: 0.8747 (m-30) cc_final: 0.7964 (p0) REVERT: A 1738 ASN cc_start: 0.8975 (m-40) cc_final: 0.8342 (m-40) REVERT: A 1796 LYS cc_start: 0.8147 (pttm) cc_final: 0.7829 (mptt) REVERT: A 1827 LEU cc_start: 0.8284 (mm) cc_final: 0.8040 (mm) REVERT: A 1841 LYS cc_start: 0.8205 (mttt) cc_final: 0.7935 (mttp) REVERT: A 1845 LEU cc_start: 0.9353 (mm) cc_final: 0.8878 (pp) REVERT: A 1894 MET cc_start: 0.7159 (ttm) cc_final: 0.6670 (ttp) REVERT: A 1897 TYR cc_start: 0.3299 (m-80) cc_final: 0.3070 (m-80) REVERT: A 1905 TYR cc_start: 0.8668 (p90) cc_final: 0.8389 (p90) REVERT: A 2162 LEU cc_start: 0.8628 (mt) cc_final: 0.8412 (mt) REVERT: A 2175 MET cc_start: 0.8542 (ttm) cc_final: 0.7322 (ttm) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.4461 time to fit residues: 429.3643 Evaluate side-chains 418 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 358 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 368 optimal weight: 6.9990 chunk 394 optimal weight: 0.1980 chunk 286 optimal weight: 8.9990 chunk 53 optimal weight: 0.0770 chunk 455 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS 5 625 ASN ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS 6 750 GLN 2 290 HIS 7 89 GLN 7 326 HIS C 50 ASN D 8 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2145 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 48430 Z= 0.160 Angle : 0.667 12.762 65697 Z= 0.341 Chirality : 0.044 0.236 7680 Planarity : 0.004 0.063 8241 Dihedral : 10.330 143.995 6979 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.34 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.50 (0.11), residues: 5814 helix: 0.48 (0.11), residues: 2380 sheet: -1.27 (0.19), residues: 700 loop : -2.33 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.002 TRP A1798 HIS 0.008 0.001 HIS 5 576 PHE 0.028 0.001 PHE B 458 TYR 0.035 0.001 TYR G 288 ARG 0.011 0.000 ARG 5 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8447 (t80) cc_final: 0.8103 (t80) REVERT: 3 129 LEU cc_start: 0.8465 (tt) cc_final: 0.8258 (mt) REVERT: 3 282 LEU cc_start: 0.9049 (mm) cc_final: 0.8765 (mm) REVERT: 3 395 ASN cc_start: 0.7639 (p0) cc_final: 0.7254 (p0) REVERT: 3 703 GLU cc_start: 0.9096 (tt0) cc_final: 0.8841 (pt0) REVERT: 4 280 MET cc_start: 0.5026 (mmm) cc_final: 0.4800 (mmm) REVERT: 4 314 MET cc_start: 0.7824 (tpt) cc_final: 0.7028 (mmm) REVERT: 4 382 MET cc_start: 0.8244 (tmm) cc_final: 0.7578 (tpp) REVERT: 4 439 PHE cc_start: 0.8441 (t80) cc_final: 0.8079 (t80) REVERT: 4 566 LEU cc_start: 0.8987 (tp) cc_final: 0.8497 (pp) REVERT: 4 637 MET cc_start: 0.8044 (mmt) cc_final: 0.7632 (mmm) REVERT: 4 749 MET cc_start: 0.8967 (mmp) cc_final: 0.8560 (mmm) REVERT: 5 68 LEU cc_start: 0.8928 (mt) cc_final: 0.8522 (tt) REVERT: 5 291 ARG cc_start: 0.7073 (mtt-85) cc_final: 0.5985 (tmt-80) REVERT: 5 404 MET cc_start: 0.2330 (ttm) cc_final: 0.2124 (ttm) REVERT: 5 478 CYS cc_start: 0.6475 (t) cc_final: 0.5977 (t) REVERT: 5 599 MET cc_start: 0.7309 (tpt) cc_final: 0.6715 (tpt) REVERT: 5 678 ASP cc_start: 0.6545 (m-30) cc_final: 0.6231 (m-30) REVERT: 5 690 ASP cc_start: 0.8476 (m-30) cc_final: 0.7999 (t0) REVERT: 6 720 ASN cc_start: 0.9241 (t0) cc_final: 0.8912 (p0) REVERT: 2 267 MET cc_start: 0.7883 (tpt) cc_final: 0.7323 (mmp) REVERT: 2 527 VAL cc_start: 0.7014 (t) cc_final: 0.6674 (t) REVERT: 2 633 LYS cc_start: 0.4094 (tptt) cc_final: 0.3723 (tptt) REVERT: 2 792 ASP cc_start: 0.9164 (m-30) cc_final: 0.8311 (t70) REVERT: 7 125 MET cc_start: 0.7882 (mmp) cc_final: 0.7616 (mmm) REVERT: 7 211 CYS cc_start: 0.8767 (t) cc_final: 0.8552 (m) REVERT: 7 402 MET cc_start: 0.9401 (mmp) cc_final: 0.9199 (mmt) REVERT: 7 621 MET cc_start: 0.8709 (ptm) cc_final: 0.8472 (tmm) REVERT: 7 675 MET cc_start: 0.6608 (mmm) cc_final: 0.6210 (mmm) REVERT: 7 711 ASP cc_start: 0.9303 (t0) cc_final: 0.9027 (p0) REVERT: C 38 ARG cc_start: 0.8833 (mtt90) cc_final: 0.8350 (mtt-85) REVERT: C 43 GLU cc_start: 0.7926 (tt0) cc_final: 0.7155 (tp30) REVERT: C 62 MET cc_start: 0.6845 (pmm) cc_final: 0.6643 (pmm) REVERT: C 77 LEU cc_start: 0.8615 (mt) cc_final: 0.8367 (mt) REVERT: C 107 LEU cc_start: 0.6425 (mt) cc_final: 0.6081 (tt) REVERT: D 8 GLN cc_start: 0.7578 (pt0) cc_final: 0.6983 (mp10) REVERT: D 180 GLU cc_start: 0.8528 (pt0) cc_final: 0.8312 (tt0) REVERT: D 188 ILE cc_start: 0.9504 (mt) cc_final: 0.9001 (tp) REVERT: E 20 PHE cc_start: 0.8780 (p90) cc_final: 0.8296 (p90) REVERT: F 202 MET cc_start: 0.7907 (mmm) cc_final: 0.7656 (tpp) REVERT: G 575 ASN cc_start: 0.8964 (t0) cc_final: 0.8720 (t0) REVERT: B 211 ILE cc_start: 0.8798 (mt) cc_final: 0.8590 (mt) REVERT: B 344 MET cc_start: 0.7200 (ptt) cc_final: 0.6871 (ptt) REVERT: B 354 ILE cc_start: 0.9164 (pt) cc_final: 0.8908 (pt) REVERT: B 483 PHE cc_start: 0.9290 (m-10) cc_final: 0.8950 (m-10) REVERT: B 639 MET cc_start: 0.8476 (mmp) cc_final: 0.7941 (mmp) REVERT: B 673 MET cc_start: 0.9006 (tpp) cc_final: 0.7509 (tpp) REVERT: A 1359 MET cc_start: 0.5346 (pmm) cc_final: 0.3658 (tpt) REVERT: A 1482 MET cc_start: 0.6511 (mpp) cc_final: 0.6013 (mmt) REVERT: A 1486 TYR cc_start: 0.8461 (t80) cc_final: 0.8124 (t80) REVERT: A 1490 PHE cc_start: 0.8538 (t80) cc_final: 0.7972 (t80) REVERT: A 1497 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8758 (mm-30) REVERT: A 1498 PHE cc_start: 0.7992 (m-10) cc_final: 0.7558 (m-10) REVERT: A 1544 GLU cc_start: 0.9469 (mp0) cc_final: 0.9173 (mp0) REVERT: A 1649 LEU cc_start: 0.9323 (mm) cc_final: 0.9004 (pp) REVERT: A 1668 MET cc_start: 0.8988 (mmp) cc_final: 0.8684 (mmm) REVERT: A 1737 ASP cc_start: 0.8720 (m-30) cc_final: 0.7942 (p0) REVERT: A 1738 ASN cc_start: 0.8966 (m-40) cc_final: 0.8314 (m-40) REVERT: A 1845 LEU cc_start: 0.9323 (mm) cc_final: 0.8853 (pp) REVERT: A 1894 MET cc_start: 0.6898 (ttm) cc_final: 0.6396 (ttp) REVERT: A 1905 TYR cc_start: 0.8665 (p90) cc_final: 0.8379 (p90) REVERT: A 2175 MET cc_start: 0.8469 (ttm) cc_final: 0.7302 (ttm) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 0.4277 time to fit residues: 412.6119 Evaluate side-chains 414 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 526 optimal weight: 9.9990 chunk 554 optimal weight: 8.9990 chunk 506 optimal weight: 4.9990 chunk 539 optimal weight: 0.9980 chunk 324 optimal weight: 5.9990 chunk 235 optimal weight: 0.7980 chunk 423 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 487 optimal weight: 0.9990 chunk 510 optimal weight: 6.9990 chunk 537 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS 5 625 ASN ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS 6 750 GLN 6 799 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 90 ASN 7 326 HIS C 82 ASN D 8 GLN ** G 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 550 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48430 Z= 0.170 Angle : 0.671 10.485 65697 Z= 0.343 Chirality : 0.044 0.285 7680 Planarity : 0.004 0.064 8241 Dihedral : 10.279 143.623 6979 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.44 (0.11), residues: 5814 helix: 0.54 (0.11), residues: 2379 sheet: -1.29 (0.19), residues: 714 loop : -2.29 (0.11), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A1798 HIS 0.007 0.001 HIS 5 576 PHE 0.027 0.001 PHE B 458 TYR 0.053 0.001 TYR A1897 ARG 0.017 0.000 ARG 5 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 524 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8458 (t80) cc_final: 0.8110 (t80) REVERT: 3 129 LEU cc_start: 0.8490 (tt) cc_final: 0.8232 (mt) REVERT: 3 282 LEU cc_start: 0.9041 (mm) cc_final: 0.8702 (mm) REVERT: 3 395 ASN cc_start: 0.7678 (p0) cc_final: 0.7283 (p0) REVERT: 3 703 GLU cc_start: 0.9123 (tt0) cc_final: 0.8898 (pt0) REVERT: 4 382 MET cc_start: 0.8365 (tmm) cc_final: 0.7753 (tpp) REVERT: 4 439 PHE cc_start: 0.8475 (t80) cc_final: 0.8101 (t80) REVERT: 4 637 MET cc_start: 0.8077 (mmt) cc_final: 0.7616 (mmm) REVERT: 4 749 MET cc_start: 0.8933 (mmp) cc_final: 0.8616 (mmm) REVERT: 5 48 ASP cc_start: 0.5873 (t0) cc_final: 0.5357 (t0) REVERT: 5 52 ASN cc_start: 0.8714 (m-40) cc_final: 0.8097 (m110) REVERT: 5 68 LEU cc_start: 0.8953 (mt) cc_final: 0.8569 (tt) REVERT: 5 291 ARG cc_start: 0.7092 (mtt-85) cc_final: 0.6016 (tmt-80) REVERT: 5 404 MET cc_start: 0.2260 (ttm) cc_final: 0.1967 (ttm) REVERT: 5 478 CYS cc_start: 0.6414 (t) cc_final: 0.5719 (t) REVERT: 5 599 MET cc_start: 0.7233 (tpt) cc_final: 0.6687 (tpt) REVERT: 5 690 ASP cc_start: 0.8486 (m-30) cc_final: 0.8036 (t0) REVERT: 6 720 ASN cc_start: 0.9252 (t0) cc_final: 0.8926 (p0) REVERT: 2 267 MET cc_start: 0.7850 (tpt) cc_final: 0.7360 (mmm) REVERT: 2 422 GLU cc_start: 0.8356 (tt0) cc_final: 0.7851 (tm-30) REVERT: 2 792 ASP cc_start: 0.8863 (m-30) cc_final: 0.8496 (t0) REVERT: 7 125 MET cc_start: 0.7843 (mmp) cc_final: 0.7566 (mmm) REVERT: 7 652 MET cc_start: 0.6396 (pmm) cc_final: 0.5768 (ptm) REVERT: 7 675 MET cc_start: 0.6629 (mmm) cc_final: 0.6241 (mmm) REVERT: 7 711 ASP cc_start: 0.9263 (t0) cc_final: 0.8984 (p0) REVERT: C 38 ARG cc_start: 0.8847 (mtt90) cc_final: 0.8341 (mtm-85) REVERT: C 43 GLU cc_start: 0.7910 (tt0) cc_final: 0.7177 (tp30) REVERT: D 8 GLN cc_start: 0.7505 (pt0) cc_final: 0.6978 (mp10) REVERT: D 138 ILE cc_start: 0.8245 (pt) cc_final: 0.7699 (pt) REVERT: D 180 GLU cc_start: 0.8599 (pt0) cc_final: 0.8323 (tt0) REVERT: D 188 ILE cc_start: 0.9390 (mt) cc_final: 0.8997 (tp) REVERT: E 20 PHE cc_start: 0.8834 (p90) cc_final: 0.8326 (p90) REVERT: F 143 TYR cc_start: 0.7690 (t80) cc_final: 0.7375 (t80) REVERT: F 202 MET cc_start: 0.7876 (mmm) cc_final: 0.7175 (tpp) REVERT: G 575 ASN cc_start: 0.8972 (t0) cc_final: 0.8734 (t0) REVERT: B 344 MET cc_start: 0.7180 (ptt) cc_final: 0.6862 (ptt) REVERT: B 483 PHE cc_start: 0.9279 (m-10) cc_final: 0.8978 (m-10) REVERT: B 639 MET cc_start: 0.8501 (mmp) cc_final: 0.7958 (mmp) REVERT: B 673 MET cc_start: 0.8875 (tpp) cc_final: 0.7270 (tpp) REVERT: A 1359 MET cc_start: 0.5417 (pmm) cc_final: 0.3671 (tpt) REVERT: A 1482 MET cc_start: 0.6513 (mpp) cc_final: 0.6010 (mmt) REVERT: A 1490 PHE cc_start: 0.8504 (t80) cc_final: 0.7945 (t80) REVERT: A 1497 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8792 (mm-30) REVERT: A 1498 PHE cc_start: 0.8005 (m-10) cc_final: 0.7565 (m-10) REVERT: A 1544 GLU cc_start: 0.9459 (mp0) cc_final: 0.9170 (mp0) REVERT: A 1649 LEU cc_start: 0.9333 (mm) cc_final: 0.9021 (pp) REVERT: A 1668 MET cc_start: 0.8990 (mmp) cc_final: 0.8631 (mmm) REVERT: A 1737 ASP cc_start: 0.8737 (m-30) cc_final: 0.7948 (p0) REVERT: A 1738 ASN cc_start: 0.8959 (m-40) cc_final: 0.8338 (m-40) REVERT: A 1845 LEU cc_start: 0.9309 (mm) cc_final: 0.8848 (pp) REVERT: A 1897 TYR cc_start: 0.4448 (m-80) cc_final: 0.3647 (m-80) REVERT: A 1905 TYR cc_start: 0.8665 (p90) cc_final: 0.8359 (p90) REVERT: A 2175 MET cc_start: 0.8635 (ttm) cc_final: 0.7487 (ttm) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.4401 time to fit residues: 403.1894 Evaluate side-chains 408 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 354 optimal weight: 5.9990 chunk 570 optimal weight: 0.7980 chunk 348 optimal weight: 8.9990 chunk 270 optimal weight: 0.2980 chunk 396 optimal weight: 1.9990 chunk 598 optimal weight: 6.9990 chunk 551 optimal weight: 30.0000 chunk 476 optimal weight: 30.0000 chunk 49 optimal weight: 0.3980 chunk 368 optimal weight: 0.0050 chunk 292 optimal weight: 7.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS 5 625 ASN ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 698 ASN 6 735 HIS 6 750 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS D 8 GLN ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 550 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2148 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 48430 Z= 0.153 Angle : 0.665 11.123 65697 Z= 0.336 Chirality : 0.044 0.195 7680 Planarity : 0.004 0.069 8241 Dihedral : 10.182 143.795 6979 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.21 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.33 (0.11), residues: 5814 helix: 0.63 (0.11), residues: 2378 sheet: -1.09 (0.20), residues: 691 loop : -2.26 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A1798 HIS 0.009 0.001 HIS 5 576 PHE 0.029 0.001 PHE B 458 TYR 0.035 0.001 TYR G 288 ARG 0.011 0.000 ARG 3 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 4.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 PHE cc_start: 0.8455 (t80) cc_final: 0.8077 (t80) REVERT: 3 282 LEU cc_start: 0.9047 (mm) cc_final: 0.8718 (mm) REVERT: 3 395 ASN cc_start: 0.7741 (p0) cc_final: 0.7363 (p0) REVERT: 3 703 GLU cc_start: 0.9109 (tt0) cc_final: 0.8895 (pt0) REVERT: 4 314 MET cc_start: 0.7711 (tpt) cc_final: 0.7348 (mmm) REVERT: 4 382 MET cc_start: 0.8306 (tmm) cc_final: 0.7761 (tpp) REVERT: 4 439 PHE cc_start: 0.8481 (t80) cc_final: 0.8076 (t80) REVERT: 4 566 LEU cc_start: 0.9018 (tp) cc_final: 0.8622 (pp) REVERT: 4 637 MET cc_start: 0.8002 (mmt) cc_final: 0.7573 (mmm) REVERT: 4 749 MET cc_start: 0.8887 (mmp) cc_final: 0.8503 (mmm) REVERT: 5 68 LEU cc_start: 0.8878 (mt) cc_final: 0.8499 (tt) REVERT: 5 278 CYS cc_start: 0.4531 (m) cc_final: 0.3977 (m) REVERT: 5 291 ARG cc_start: 0.6987 (mtt-85) cc_final: 0.5986 (tmt-80) REVERT: 5 404 MET cc_start: 0.2726 (ttm) cc_final: 0.2360 (ttm) REVERT: 5 478 CYS cc_start: 0.6356 (t) cc_final: 0.5708 (t) REVERT: 5 599 MET cc_start: 0.7269 (tpt) cc_final: 0.6712 (tpt) REVERT: 5 690 ASP cc_start: 0.8401 (m-30) cc_final: 0.8027 (t0) REVERT: 6 720 ASN cc_start: 0.9207 (t0) cc_final: 0.8902 (p0) REVERT: 2 237 MET cc_start: 0.5905 (mmm) cc_final: 0.5296 (tpt) REVERT: 2 267 MET cc_start: 0.7813 (tpt) cc_final: 0.7321 (mmp) REVERT: 2 527 VAL cc_start: 0.6832 (t) cc_final: 0.6478 (t) REVERT: 2 597 VAL cc_start: 0.7460 (t) cc_final: 0.7128 (p) REVERT: 2 633 LYS cc_start: 0.3968 (tptt) cc_final: 0.3761 (tptt) REVERT: 2 658 ASN cc_start: 0.8460 (p0) cc_final: 0.8185 (p0) REVERT: 2 792 ASP cc_start: 0.8851 (m-30) cc_final: 0.8460 (t0) REVERT: 7 125 MET cc_start: 0.7834 (mmp) cc_final: 0.7555 (mmm) REVERT: 7 652 MET cc_start: 0.6239 (pmm) cc_final: 0.5761 (ptm) REVERT: 7 675 MET cc_start: 0.6486 (mmm) cc_final: 0.6088 (mmm) REVERT: 7 711 ASP cc_start: 0.9210 (t0) cc_final: 0.8919 (p0) REVERT: C 43 GLU cc_start: 0.7796 (tt0) cc_final: 0.7069 (tp30) REVERT: C 62 MET cc_start: 0.6976 (pmm) cc_final: 0.6403 (tpt) REVERT: D 8 GLN cc_start: 0.7543 (pt0) cc_final: 0.7073 (mp10) REVERT: D 180 GLU cc_start: 0.8521 (pt0) cc_final: 0.8268 (tt0) REVERT: D 188 ILE cc_start: 0.9342 (mt) cc_final: 0.9081 (tp) REVERT: E 20 PHE cc_start: 0.8823 (p90) cc_final: 0.8307 (p90) REVERT: E 105 PHE cc_start: 0.7974 (m-80) cc_final: 0.7729 (m-80) REVERT: E 168 LYS cc_start: 0.7975 (ptpt) cc_final: 0.7773 (ptmt) REVERT: F 202 MET cc_start: 0.7659 (mmm) cc_final: 0.7211 (tpp) REVERT: G 473 TRP cc_start: 0.6082 (m-10) cc_final: 0.5718 (m-10) REVERT: G 541 ASN cc_start: 0.8838 (t0) cc_final: 0.8613 (t0) REVERT: G 575 ASN cc_start: 0.8913 (t0) cc_final: 0.8697 (t0) REVERT: B 188 MET cc_start: 0.8210 (mmp) cc_final: 0.7979 (mmm) REVERT: B 344 MET cc_start: 0.7029 (ptt) cc_final: 0.6756 (ptt) REVERT: B 354 ILE cc_start: 0.9200 (mp) cc_final: 0.8902 (mp) REVERT: B 460 ASN cc_start: 0.9352 (m-40) cc_final: 0.9140 (m-40) REVERT: B 483 PHE cc_start: 0.9260 (m-10) cc_final: 0.8922 (m-10) REVERT: B 639 MET cc_start: 0.8065 (mmp) cc_final: 0.7722 (mmp) REVERT: B 673 MET cc_start: 0.8843 (tpp) cc_final: 0.7340 (tpp) REVERT: A 1359 MET cc_start: 0.5219 (pmm) cc_final: 0.3536 (tpt) REVERT: A 1482 MET cc_start: 0.6547 (mpp) cc_final: 0.6085 (mmt) REVERT: A 1490 PHE cc_start: 0.8501 (t80) cc_final: 0.7906 (t80) REVERT: A 1497 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8771 (mm-30) REVERT: A 1498 PHE cc_start: 0.7894 (m-10) cc_final: 0.7514 (m-10) REVERT: A 1544 GLU cc_start: 0.9424 (mp0) cc_final: 0.9170 (mp0) REVERT: A 1649 LEU cc_start: 0.9388 (mm) cc_final: 0.9086 (pp) REVERT: A 1668 MET cc_start: 0.9050 (mmp) cc_final: 0.8737 (mmm) REVERT: A 1737 ASP cc_start: 0.8660 (m-30) cc_final: 0.7822 (p0) REVERT: A 1738 ASN cc_start: 0.8945 (m-40) cc_final: 0.8321 (m-40) REVERT: A 1845 LEU cc_start: 0.9378 (mm) cc_final: 0.8962 (pp) REVERT: A 1897 TYR cc_start: 0.3914 (m-80) cc_final: 0.3654 (m-80) REVERT: A 1905 TYR cc_start: 0.8688 (p90) cc_final: 0.8380 (p90) REVERT: A 2175 MET cc_start: 0.8619 (ttm) cc_final: 0.7489 (ttm) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.4523 time to fit residues: 418.9518 Evaluate side-chains 412 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 378 optimal weight: 6.9990 chunk 507 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 439 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 477 optimal weight: 60.0000 chunk 199 optimal weight: 6.9990 chunk 490 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 203 ASN 5 284 ASN 5 576 HIS 5 625 ASN ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS 6 750 GLN 7 326 HIS D 8 GLN ** G 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 ASN G 550 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.090371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.072500 restraints weight = 306952.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.073484 restraints weight = 240773.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.073911 restraints weight = 182880.793| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 48430 Z= 0.186 Angle : 0.674 13.802 65697 Z= 0.344 Chirality : 0.044 0.243 7680 Planarity : 0.004 0.077 8241 Dihedral : 10.185 139.239 6979 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.69 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.27 (0.11), residues: 5814 helix: 0.66 (0.11), residues: 2394 sheet: -1.03 (0.20), residues: 689 loop : -2.24 (0.11), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A1798 HIS 0.009 0.001 HIS 3 175 PHE 0.026 0.001 PHE B 458 TYR 0.041 0.001 TYR F 201 ARG 0.027 0.001 ARG 3 700 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8505.59 seconds wall clock time: 149 minutes 15.47 seconds (8955.47 seconds total)