Starting phenix.real_space_refine on Mon Dec 30 19:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kg9_37215/12_2024/8kg9_37215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kg9_37215/12_2024/8kg9_37215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kg9_37215/12_2024/8kg9_37215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kg9_37215/12_2024/8kg9_37215.map" model { file = "/net/cci-nas-00/data/ceres_data/8kg9_37215/12_2024/8kg9_37215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kg9_37215/12_2024/8kg9_37215.cif" } resolution = 4.52 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= 0.008 sd= 0.054 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: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 33 5.49 5 Mg 4 5.21 5 S 283 5.16 5 C 40251 2.51 5 N 10862 2.21 5 O 12067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 63507 Number of models: 1 Model: "" Number of chains: 25 Chain: "2" Number of atoms: 5270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5270 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 641} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "3" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4948 Classifications: {'peptide': 637} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "4" Number of atoms: 5390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5390 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 652} Chain breaks: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5325 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "6" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4955 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 605} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4945 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 30, 'TRANS': 605} Chain breaks: 6 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'TYR:plan': 2, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1633 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1617 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1387 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2004 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4599 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 552} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3380 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3411 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 307 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain breaks: 1 Chain: "J" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 159 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "M" Number of atoms: 6447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6447 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 31, 'TRANS': 780} Chain breaks: 5 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4199 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 29, 'TRANS': 499} Chain breaks: 5 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" 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 1339 SG CYS 2 341 88.539 159.415 134.540 1.00361.23 S ATOM 1362 SG CYS 2 344 88.192 163.284 134.982 1.00359.77 S ATOM 1520 SG CYS 2 364 91.650 161.275 134.619 1.00432.54 S ATOM 1541 SG CYS 2 367 89.760 161.337 137.696 1.00426.58 S ATOM 11669 SG CYS 4 349 101.072 155.894 172.964 1.00753.81 S ATOM 11690 SG CYS 4 352 103.538 158.751 172.296 1.00722.63 S ATOM 11837 SG CYS 4 371 99.939 159.112 174.042 1.00756.28 S ATOM 11879 SG CYS 4 376 100.110 159.106 170.623 1.00753.01 S ATOM 16761 SG CYS 5 183 66.266 160.127 133.869 1.00293.23 S ATOM 16786 SG CYS 5 186 64.203 163.370 133.844 1.00313.59 S ATOM 16956 SG CYS 5 211 67.707 163.864 133.724 1.00293.92 S ATOM 16984 SG CYS 5 236 66.476 162.424 136.880 1.00331.27 S ATOM 22369 SG CYS 6 333 101.547 159.733 149.880 1.00484.66 S ATOM 22403 SG CYS 6 338 100.798 163.691 147.854 1.00520.34 S ATOM 27422 SG CYS 7 262 76.546 154.613 178.537 1.00646.02 S ATOM 27445 SG CYS 7 265 74.011 155.717 180.657 1.00624.90 S ATOM 27595 SG CYS 7 284 73.697 156.783 176.980 1.00625.93 S ATOM 27632 SG CYS 7 289 76.188 158.513 178.967 1.00570.45 S ATOM 58722 SG CYS M2164 68.498 73.461 96.578 1.00903.10 S ATOM 58745 SG CYS M2167 67.638 70.863 98.952 1.00961.29 S ATOM 58846 SG CYS M2179 64.963 72.760 97.214 1.00879.63 S ATOM 58859 SG CYS M2181 67.685 74.427 100.068 1.00889.30 S ATOM 58262 SG CYS M2108 86.551 41.827 65.457 1.00999.99 S ATOM 58289 SG CYS M2111 87.470 40.436 68.830 1.00999.99 S ATOM 58438 SG CYS M2130 89.894 42.767 67.105 1.00999.99 S ATOM 58462 SG CYS M2133 89.564 39.418 65.716 1.00999.99 S Time building chain proxies: 26.20, per 1000 atoms: 0.41 Number of scatterers: 63507 At special positions: 0 Unit cell: (152.64, 246.98, 226.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 283 16.00 P 33 15.00 Mg 4 11.99 O 12067 8.00 N 10862 7.00 C 40251 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.28 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 344 " pdb=" ZN 41400 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 352 " pdb=" ZN 5 802 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 183 " pdb=" ZN 61400 " pdb="ZN ZN 61400 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61400 " - pdb=" SG CYS 6 338 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb=" ZN M3000 " pdb="ZN ZN M3000 " - pdb=" SG CYS M2164 " pdb="ZN ZN M3000 " - pdb=" SG CYS M2167 " pdb="ZN ZN M3000 " - pdb=" SG CYS M2179 " pdb="ZN ZN M3000 " - pdb=" SG CYS M2181 " pdb=" ZN M3001 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2130 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2133 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2108 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2111 " Number of angles added : 36 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15080 Finding SS restraints... Secondary structure from input PDB file: 272 helices and 81 sheets defined 45.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 Processing helix chain '2' and resid 193 through 200 Processing helix chain '2' and resid 200 through 217 removed outlier: 3.758A pdb=" N LEU 2 216 " --> pdb=" O LYS 2 212 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 231 Processing helix chain '2' and resid 232 through 238 Processing helix chain '2' and resid 254 through 263 Processing helix chain '2' and resid 263 through 283 removed outlier: 4.514A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) Processing helix chain '2' and resid 305 through 309 Processing helix chain '2' and resid 310 through 314 Processing helix chain '2' and resid 435 through 443 removed outlier: 3.659A pdb=" N ASN 2 439 " --> pdb=" O ASP 2 435 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 490 Processing helix chain '2' and resid 492 through 501 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 557 Processing helix chain '2' and resid 572 through 577 Processing helix chain '2' and resid 594 through 600 Processing helix chain '2' and resid 608 through 612 Processing helix chain '2' and resid 613 through 626 removed outlier: 3.847A pdb=" N GLN 2 626 " --> pdb=" O GLU 2 622 " (cutoff:3.500A) Processing helix chain '2' and resid 652 through 656 removed outlier: 3.939A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 670 through 677 removed outlier: 3.938A pdb=" N LEU 2 674 " --> pdb=" O THR 2 670 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 707 Processing helix chain '2' and resid 739 through 755 Processing helix chain '2' and resid 759 through 774 Processing helix chain '2' and resid 782 through 794 Processing helix chain '2' and resid 806 through 825 Processing helix chain '2' and resid 830 through 849 Processing helix chain '2' and resid 850 through 866 removed outlier: 4.172A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 2 866 " --> pdb=" O ALA 2 862 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 35 Processing helix chain '3' and resid 35 through 55 removed outlier: 4.064A pdb=" N ARG 3 39 " --> pdb=" O PHE 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 removed outlier: 3.586A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 138 Proline residue: 3 123 - end of helix removed outlier: 4.249A pdb=" N ASP 3 138 " --> pdb=" O ASP 3 134 " (cutoff:3.500A) Processing helix chain '3' and resid 143 through 150 removed outlier: 3.523A pdb=" N SER 3 149 " --> pdb=" O SER 3 145 " (cutoff:3.500A) Processing helix chain '3' and resid 302 through 306 Processing helix chain '3' and resid 343 through 349 Processing helix chain '3' and resid 350 through 356 removed outlier: 3.597A pdb=" N LYS 3 356 " --> pdb=" O LYS 3 352 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 367 Processing helix chain '3' and resid 374 through 386 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 438 through 444 Processing helix chain '3' and resid 461 through 466 Processing helix chain '3' and resid 479 through 493 removed outlier: 5.086A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 533 Processing helix chain '3' and resid 554 through 571 Processing helix chain '3' and resid 652 through 667 Processing helix chain '3' and resid 672 through 688 removed outlier: 4.289A pdb=" N ASP 3 685 " --> pdb=" O LYS 3 681 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN 3 688 " --> pdb=" O THR 3 684 " (cutoff:3.500A) Processing helix chain '3' and resid 697 through 717 removed outlier: 3.602A pdb=" N THR 3 701 " --> pdb=" O ILE 3 697 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 739 Processing helix chain '4' and resid 186 through 195 removed outlier: 3.574A pdb=" N CYS 4 190 " --> pdb=" O SER 4 186 " (cutoff:3.500A) Processing helix chain '4' and resid 217 through 223 removed outlier: 3.971A pdb=" N GLU 4 223 " --> pdb=" O THR 4 219 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 235 removed outlier: 3.921A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 251 removed outlier: 3.577A pdb=" N TYR 4 251 " --> pdb=" O ASN 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 251 through 264 removed outlier: 3.562A pdb=" N ASP 4 256 " --> pdb=" O LYS 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 287 removed outlier: 3.893A pdb=" N VAL 4 285 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 299 Processing helix chain '4' and resid 506 through 515 Processing helix chain '4' and resid 517 through 526 Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 571 through 583 Processing helix chain '4' and resid 637 through 652 removed outlier: 4.069A pdb=" N THR 4 641 " --> pdb=" O MET 4 637 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 701 removed outlier: 4.160A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 713 through 731 removed outlier: 3.551A pdb=" N ASP 4 731 " --> pdb=" O LEU 4 727 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 758 removed outlier: 4.094A pdb=" N THR 4 748 " --> pdb=" O VAL 4 744 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 780 Processing helix chain '4' and resid 794 through 811 Processing helix chain '4' and resid 812 through 814 No H-bonds generated for 'chain '4' and resid 812 through 814' Processing helix chain '4' and resid 818 through 835 removed outlier: 3.528A pdb=" N ASP 4 835 " --> pdb=" O SER 4 831 " (cutoff:3.500A) Processing helix chain '4' and resid 846 through 850 Processing helix chain '4' and resid 857 through 876 Processing helix chain '4' and resid 882 through 893 removed outlier: 3.669A pdb=" N ASN 4 891 " --> pdb=" O ILE 4 887 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU 4 892 " --> pdb=" O LYS 4 888 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS 4 893 " --> pdb=" O GLN 4 889 " (cutoff:3.500A) Processing helix chain '4' and resid 899 through 913 removed outlier: 4.211A pdb=" N ILE 4 903 " --> pdb=" O GLU 4 899 " (cutoff:3.500A) Processing helix chain '5' and resid 21 through 37 Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 82 removed outlier: 3.688A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU 5 82 " --> pdb=" O LYS 5 78 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 103 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 184 through 187 Processing helix chain '5' and resid 349 through 363 removed outlier: 3.519A pdb=" N GLU 5 354 " --> pdb=" O THR 5 350 " (cutoff:3.500A) Processing helix chain '5' and resid 364 through 374 removed outlier: 4.156A pdb=" N GLU 5 368 " --> pdb=" O PRO 5 364 " (cutoff:3.500A) Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 467 through 473 Processing helix chain '5' and resid 486 through 500 removed outlier: 3.946A pdb=" N ARG 5 490 " --> pdb=" O ARG 5 486 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 505 through 509 removed outlier: 3.720A pdb=" N GLY 5 508 " --> pdb=" O ALA 5 505 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 540 Processing helix chain '5' and resid 543 through 551 Processing helix chain '5' and resid 561 through 577 Processing helix chain '5' and resid 577 through 592 removed outlier: 3.909A pdb=" N MET 5 583 " --> pdb=" O ASN 5 579 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY 5 591 " --> pdb=" O GLN 5 587 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 611 Processing helix chain '5' and resid 617 through 640 removed outlier: 4.598A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER 5 624 " --> pdb=" O GLU 5 620 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL 5 627 " --> pdb=" O SER 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 644 through 650 removed outlier: 4.344A pdb=" N ILE 5 648 " --> pdb=" O SER 5 644 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR 5 649 " --> pdb=" O SER 5 645 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE 5 650 " --> pdb=" O ILE 5 646 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 644 through 650' Processing helix chain '5' and resid 650 through 667 removed outlier: 3.613A pdb=" N THR 5 660 " --> pdb=" O ILE 5 656 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA 5 664 " --> pdb=" O THR 5 660 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 694 removed outlier: 4.182A pdb=" N VAL 5 677 " --> pdb=" O GLN 5 673 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA 5 692 " --> pdb=" O THR 5 688 " (cutoff:3.500A) Processing helix chain '5' and resid 707 through 720 removed outlier: 3.958A pdb=" N ILE 5 711 " --> pdb=" O SER 5 707 " (cutoff:3.500A) Processing helix chain '5' and resid 730 through 740 removed outlier: 6.340A pdb=" N PHE 5 737 " --> pdb=" O LEU 5 733 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL 5 738 " --> pdb=" O ARG 5 734 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP 5 739 " --> pdb=" O ARG 5 735 " (cutoff:3.500A) Processing helix chain '5' and resid 740 through 746 removed outlier: 3.702A pdb=" N GLN 5 745 " --> pdb=" O HIS 5 741 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU 5 746 " --> pdb=" O ARG 5 742 " (cutoff:3.500A) Processing helix chain '5' and resid 746 through 759 removed outlier: 4.639A pdb=" N LYS 5 757 " --> pdb=" O TYR 5 753 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS 5 758 " --> pdb=" O ALA 5 754 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 120 removed outlier: 4.837A pdb=" N GLU 6 116 " --> pdb=" O ARG 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 138 through 147 Processing helix chain '6' and resid 154 through 159 Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 178 through 192 removed outlier: 4.939A pdb=" N ARG 6 186 " --> pdb=" O GLN 6 182 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG 6 187 " --> pdb=" O LYS 6 183 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL 6 189 " --> pdb=" O LEU 6 185 " (cutoff:3.500A) Processing helix chain '6' and resid 382 through 389 Processing helix chain '6' and resid 500 through 508 Processing helix chain '6' and resid 509 through 522 Processing helix chain '6' and resid 524 through 533 removed outlier: 3.658A pdb=" N LEU 6 529 " --> pdb=" O ILE 6 525 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL 6 530 " --> pdb=" O TYR 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 553 Processing helix chain '6' and resid 580 through 592 Processing helix chain '6' and resid 626 through 632 Processing helix chain '6' and resid 645 through 657 removed outlier: 4.310A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE 6 652 " --> pdb=" O ASP 6 648 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 702 through 709 Processing helix chain '6' and resid 722 through 735 removed outlier: 3.614A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA 6 728 " --> pdb=" O ASP 6 724 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER 6 729 " --> pdb=" O THR 6 725 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL 6 732 " --> pdb=" O ALA 6 728 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP 6 733 " --> pdb=" O SER 6 729 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 761 removed outlier: 3.620A pdb=" N PHE 6 761 " --> pdb=" O TYR 6 757 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 784 Processing helix chain '6' and resid 787 through 791 removed outlier: 4.023A pdb=" N ARG 6 790 " --> pdb=" O GLY 6 787 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 810 Processing helix chain '6' and resid 820 through 834 Processing helix chain '7' and resid 13 through 28 Processing helix chain '7' and resid 29 through 34 Processing helix chain '7' and resid 61 through 73 Processing helix chain '7' and resid 82 through 96 Processing helix chain '7' and resid 98 through 100 No H-bonds generated for 'chain '7' and resid 98 through 100' Processing helix chain '7' and resid 101 through 109 Processing helix chain '7' and resid 110 through 123 Processing helix chain '7' and resid 136 through 145 Processing helix chain '7' and resid 193 through 198 Processing helix chain '7' and resid 213 through 217 Processing helix chain '7' and resid 231 through 235 Processing helix chain '7' and resid 286 through 291 Processing helix chain '7' and resid 292 through 294 No H-bonds generated for 'chain '7' and resid 292 through 294' Processing helix chain '7' and resid 363 through 369 Processing helix chain '7' and resid 397 through 409 removed outlier: 3.769A pdb=" N MET 7 402 " --> pdb=" O GLU 7 398 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 419 removed outlier: 4.135A pdb=" N ALA 7 419 " --> pdb=" O ALA 7 415 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 removed outlier: 3.566A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL 7 437 " --> pdb=" O LEU 7 433 " (cutoff:3.500A) Processing helix chain '7' and resid 471 through 477 removed outlier: 3.786A pdb=" N LYS 7 475 " --> pdb=" O LYS 7 471 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE 7 476 " --> pdb=" O ALA 7 472 " (cutoff:3.500A) Processing helix chain '7' and resid 499 through 503 removed outlier: 4.402A pdb=" N THR 7 503 " --> pdb=" O ASP 7 500 " (cutoff:3.500A) Processing helix chain '7' and resid 511 through 516 removed outlier: 3.887A pdb=" N LEU 7 515 " --> pdb=" O GLY 7 511 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA 7 516 " --> pdb=" O ALA 7 512 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 511 through 516' Processing helix chain '7' and resid 530 through 544 Processing helix chain '7' and resid 569 through 573 removed outlier: 3.636A pdb=" N ARG 7 573 " --> pdb=" O LEU 7 570 " (cutoff:3.500A) Processing helix chain '7' and resid 587 through 594 removed outlier: 3.589A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 607 through 620 removed outlier: 3.649A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 644 Processing helix chain '7' and resid 653 through 673 Processing helix chain '7' and resid 685 through 703 removed outlier: 3.636A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 729 Processing helix chain 'A' and resid 2 through 23 removed outlier: 3.674A pdb=" N GLY A 6 " --> pdb=" O TYR A 2 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 61 Processing helix chain 'A' and resid 67 through 105 Processing helix chain 'A' and resid 124 through 143 Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.940A pdb=" N VAL A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.971A pdb=" N LEU B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 94 through 108 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 137 through 162 removed outlier: 3.544A pdb=" N LEU B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 200 Proline residue: B 183 - end of helix Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 26 through 32 removed outlier: 4.372A pdb=" N TYR C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.235A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 117 through 141 Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 170 through 193 removed outlier: 3.596A pdb=" N LYS C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 removed outlier: 3.642A pdb=" N GLU D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 80 through 107 Processing helix chain 'D' and resid 123 through 154 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 176 through 199 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 203 through 207 removed outlier: 3.772A pdb=" N GLN D 207 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 289 removed outlier: 4.303A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 19 removed outlier: 4.354A pdb=" N GLU E 10 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 53 Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 130 through 136 Processing helix chain 'E' and resid 146 through 152 removed outlier: 3.763A pdb=" N THR E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 165 Processing helix chain 'E' and resid 224 through 241 Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.567A pdb=" N GLN E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 284 removed outlier: 4.302A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 303 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 352 through 367 Processing helix chain 'E' and resid 369 through 375 Processing helix chain 'E' and resid 381 through 386 Processing helix chain 'E' and resid 387 through 400 removed outlier: 4.377A pdb=" N ASP E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 462 through 485 removed outlier: 3.897A pdb=" N ASP E 485 " --> pdb=" O TRP E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 516 Processing helix chain 'E' and resid 535 through 541 removed outlier: 3.679A pdb=" N ASN E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 559 Processing helix chain 'E' and resid 594 through 599 Processing helix chain 'E' and resid 603 through 615 removed outlier: 4.345A pdb=" N MET E 607 " --> pdb=" O ASN E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 647 removed outlier: 4.373A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'F' and resid 671 through 680 Processing helix chain 'F' and resid 723 through 733 Processing helix chain 'F' and resid 782 through 791 Processing helix chain 'F' and resid 818 through 844 Processing helix chain 'F' and resid 850 through 877 Processing helix chain 'F' and resid 878 through 889 Processing helix chain 'F' and resid 891 through 905 Processing helix chain 'F' and resid 907 through 923 removed outlier: 3.759A pdb=" N VAL F 911 " --> pdb=" O LEU F 907 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 923 " --> pdb=" O GLU F 919 " (cutoff:3.500A) Processing helix chain 'G' and resid 671 through 680 Processing helix chain 'G' and resid 724 through 735 removed outlier: 5.454A pdb=" N SER G 732 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLY G 733 " --> pdb=" O TRP G 729 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS G 735 " --> pdb=" O MET G 731 " (cutoff:3.500A) Processing helix chain 'G' and resid 782 through 790 Processing helix chain 'G' and resid 818 through 845 Processing helix chain 'G' and resid 850 through 877 Processing helix chain 'G' and resid 878 through 889 removed outlier: 3.515A pdb=" N GLU G 888 " --> pdb=" O SER G 884 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 889 " --> pdb=" O LEU G 885 " (cutoff:3.500A) Processing helix chain 'G' and resid 891 through 905 Processing helix chain 'G' and resid 907 through 923 removed outlier: 3.781A pdb=" N VAL G 911 " --> pdb=" O LEU G 907 " (cutoff:3.500A) Processing helix chain 'H' and resid 671 through 680 Processing helix chain 'H' and resid 723 through 732 Processing helix chain 'H' and resid 782 through 790 Processing helix chain 'H' and resid 818 through 844 Processing helix chain 'H' and resid 850 through 877 Processing helix chain 'H' and resid 878 through 889 removed outlier: 3.613A pdb=" N ALA H 882 " --> pdb=" O ASN H 878 " (cutoff:3.500A) Processing helix chain 'H' and resid 891 through 906 Processing helix chain 'H' and resid 907 through 923 Processing helix chain 'M' and resid 1364 through 1369 Processing helix chain 'M' and resid 1433 through 1442 Processing helix chain 'M' and resid 1525 through 1539 Processing helix chain 'M' and resid 1539 through 1548 removed outlier: 4.385A pdb=" N THR M1545 " --> pdb=" O GLY M1541 " (cutoff:3.500A) Processing helix chain 'M' and resid 1565 through 1580 removed outlier: 3.518A pdb=" N LEU M1569 " --> pdb=" O ASP M1565 " (cutoff:3.500A) Processing helix chain 'M' and resid 1594 through 1605 removed outlier: 4.454A pdb=" N LYS M1599 " --> pdb=" O PRO M1595 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU M1600 " --> pdb=" O PHE M1596 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY M1602 " --> pdb=" O THR M1598 " (cutoff:3.500A) Processing helix chain 'M' and resid 1627 through 1657 removed outlier: 3.537A pdb=" N LYS M1633 " --> pdb=" O PRO M1629 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY M1643 " --> pdb=" O VAL M1639 " (cutoff:3.500A) Processing helix chain 'M' and resid 1668 through 1683 removed outlier: 3.581A pdb=" N GLU M1683 " --> pdb=" O LYS M1679 " (cutoff:3.500A) Processing helix chain 'M' and resid 1706 through 1714 removed outlier: 3.793A pdb=" N MET M1713 " --> pdb=" O THR M1709 " (cutoff:3.500A) Processing helix chain 'M' and resid 1738 through 1748 removed outlier: 3.600A pdb=" N ALA M1748 " --> pdb=" O ILE M1744 " (cutoff:3.500A) Processing helix chain 'M' and resid 1785 through 1803 Processing helix chain 'M' and resid 1806 through 1822 removed outlier: 3.705A pdb=" N ASP M1810 " --> pdb=" O ASN M1806 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA M1817 " --> pdb=" O VAL M1813 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER M1818 " --> pdb=" O ASN M1814 " (cutoff:3.500A) Processing helix chain 'M' and resid 1829 through 1854 removed outlier: 3.854A pdb=" N LEU M1854 " --> pdb=" O GLU M1850 " (cutoff:3.500A) Processing helix chain 'M' and resid 1876 through 1892 removed outlier: 3.700A pdb=" N ALA M1880 " --> pdb=" O GLU M1876 " (cutoff:3.500A) Processing helix chain 'M' and resid 1939 through 1945 Processing helix chain 'M' and resid 1948 through 1976 removed outlier: 4.071A pdb=" N GLU M1952 " --> pdb=" O ILE M1948 " (cutoff:3.500A) Processing helix chain 'M' and resid 1998 through 2026 removed outlier: 3.519A pdb=" N HIS M2005 " --> pdb=" O ASN M2001 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS M2009 " --> pdb=" O HIS M2005 " (cutoff:3.500A) Proline residue: M2010 - end of helix removed outlier: 3.800A pdb=" N GLU M2024 " --> pdb=" O LYS M2020 " (cutoff:3.500A) Processing helix chain 'M' and resid 2028 through 2036 removed outlier: 3.745A pdb=" N ASP M2034 " --> pdb=" O GLN M2030 " (cutoff:3.500A) Processing helix chain 'M' and resid 2049 through 2063 Processing helix chain 'M' and resid 2064 through 2065 No H-bonds generated for 'chain 'M' and resid 2064 through 2065' Processing helix chain 'M' and resid 2066 through 2067 No H-bonds generated for 'chain 'M' and resid 2066 through 2067' Processing helix chain 'M' and resid 2068 through 2083 Processing helix chain 'M' and resid 2123 through 2129 removed outlier: 3.643A pdb=" N PHE M2128 " --> pdb=" O PRO M2124 " (cutoff:3.500A) Processing helix chain 'M' and resid 2138 through 2159 Processing helix chain 'M' and resid 2190 through 2208 removed outlier: 4.206A pdb=" N ILE M2194 " --> pdb=" O PRO M2190 " (cutoff:3.500A) Processing helix chain 'M' and resid 2210 through 2222 removed outlier: 3.530A pdb=" N ILE M2222 " --> pdb=" O ALA M2218 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 30 removed outlier: 3.704A pdb=" N LEU N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Proline residue: N 19 - end of helix removed outlier: 3.879A pdb=" N ARG N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 48 Processing helix chain 'N' and resid 54 through 70 Processing helix chain 'N' and resid 79 through 98 Processing helix chain 'N' and resid 210 through 237 removed outlier: 3.914A pdb=" N PHE N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 276 removed outlier: 3.946A pdb=" N LEU N 275 " --> pdb=" O ILE N 271 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY N 276 " --> pdb=" O LYS N 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 360 Processing helix chain 'N' and resid 382 through 394 Processing helix chain 'N' and resid 410 through 427 removed outlier: 3.761A pdb=" N ASP N 426 " --> pdb=" O GLN N 422 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP N 427 " --> pdb=" O LYS N 423 " (cutoff:3.500A) Processing helix chain 'N' and resid 453 through 464 Processing helix chain 'N' and resid 465 through 472 removed outlier: 3.546A pdb=" N PHE N 472 " --> pdb=" O LEU N 468 " (cutoff:3.500A) Processing helix chain 'N' and resid 509 through 514 Processing helix chain 'N' and resid 515 through 520 Processing helix chain 'N' and resid 545 through 554 Processing helix chain 'N' and resid 595 through 610 removed outlier: 3.521A pdb=" N GLY N 610 " --> pdb=" O ILE N 606 " (cutoff:3.500A) Processing helix chain 'N' and resid 626 through 631 removed outlier: 3.683A pdb=" N LEU N 630 " --> pdb=" O LEU N 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 317 through 319 removed outlier: 7.484A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE 2 429 " --> pdb=" O GLU 2 452 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU 2 452 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N LEU 2 411 " --> pdb=" O SER 2 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 333 through 334 Processing sheet with id=AA3, first strand: chain '2' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain '2' and resid 339 through 341 Processing sheet with id=AA5, first strand: chain '2' and resid 525 through 527 Processing sheet with id=AA6, first strand: chain '2' and resid 563 through 566 removed outlier: 6.398A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 579 through 583 Processing sheet with id=AA8, first strand: chain '2' and resid 628 through 630 Processing sheet with id=AA9, first strand: chain '3' and resid 95 through 97 Processing sheet with id=AB1, first strand: chain '3' and resid 273 through 277 removed outlier: 6.682A pdb=" N ARG 3 255 " --> pdb=" O THR 3 189 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR 3 189 " --> pdb=" O ARG 3 255 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR 3 257 " --> pdb=" O THR 3 187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR 3 187 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN 3 293 " --> pdb=" O VAL 3 326 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL 3 326 " --> pdb=" O ASN 3 293 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL 3 295 " --> pdb=" O ASN 3 324 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS 3 318 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 198 through 201 Processing sheet with id=AB3, first strand: chain '3' and resid 469 through 473 removed outlier: 3.688A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN 3 404 " --> pdb=" O LEU 3 545 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE 3 547 " --> pdb=" O ASN 3 404 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 494 through 495 Processing sheet with id=AB5, first strand: chain '4' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain '4' and resid 339 through 342 removed outlier: 10.009A pdb=" N SER 4 414 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N VAL 4 461 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER 4 416 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL 4 463 " --> pdb=" O SER 4 416 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS 4 418 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N HIS 4 465 " --> pdb=" O CYS 4 418 " (cutoff:3.500A) removed outlier: 10.663A pdb=" N TYR 4 420 " --> pdb=" O HIS 4 465 " (cutoff:3.500A) removed outlier: 14.836A pdb=" N LYS 4 467 " --> pdb=" O TYR 4 420 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 355 through 359 removed outlier: 3.586A pdb=" N VAL 4 358 " --> pdb=" O ALA 4 345 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 444 through 445 removed outlier: 4.379A pdb=" N ILE 4 444 " --> pdb=" O LYS 4 454 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 591 through 592 removed outlier: 6.603A pdb=" N THR 4 591 " --> pdb=" O ASP 4 632 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS 4 629 " --> pdb=" O SER 4 670 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU 4 672 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 604 through 606 Processing sheet with id=AC2, first strand: chain '4' and resid 654 through 658 Processing sheet with id=AC3, first strand: chain '4' and resid 761 through 762 removed outlier: 6.454A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 60 through 64 Processing sheet with id=AC5, first strand: chain '5' and resid 189 through 192 removed outlier: 6.339A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 189 through 192 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 173 through 182 current: chain '5' and resid 325 through 335 removed outlier: 6.905A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AC8, first strand: chain '5' and resid 415 through 416 removed outlier: 6.904A pdb=" N LEU 5 415 " --> pdb=" O VAL 5 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '5' and resid 439 through 440 removed outlier: 7.483A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 451 through 456 removed outlier: 5.514A pdb=" N GLU 5 461 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '5' and resid 501 through 503 Processing sheet with id=AD3, first strand: chain '6' and resid 151 through 152 removed outlier: 6.763A pdb=" N ILE 6 151 " --> pdb=" O SER 6 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '6' and resid 286 through 290 removed outlier: 3.791A pdb=" N ILE 6 402 " --> pdb=" O SER 6 453 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER 6 453 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR 6 295 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 6 293 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL 6 294 " --> pdb=" O ASP 6 393 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 286 through 290 Processing sheet with id=AD6, first strand: chain '6' and resid 557 through 558 Processing sheet with id=AD7, first strand: chain '6' and resid 570 through 571 Processing sheet with id=AD8, first strand: chain '6' and resid 596 through 598 removed outlier: 6.561A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain '6' and resid 660 through 661 Processing sheet with id=AE1, first strand: chain '6' and resid 764 through 765 removed outlier: 5.928A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain '7' and resid 80 through 81 removed outlier: 7.548A pdb=" N ILE 7 80 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain '7' and resid 238 through 241 Processing sheet with id=AE4, first strand: chain '7' and resid 244 through 248 removed outlier: 6.761A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 7 248 " --> pdb=" O GLU 7 312 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU 7 312 " --> pdb=" O VAL 7 248 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '7' and resid 244 through 248 removed outlier: 6.761A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 7 248 " --> pdb=" O GLU 7 312 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU 7 312 " --> pdb=" O VAL 7 248 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 268 through 272 removed outlier: 3.547A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '7' and resid 357 through 358 removed outlier: 3.994A pdb=" N GLU 7 373 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '7' and resid 456 through 458 Processing sheet with id=AE9, first strand: chain '7' and resid 480 through 482 removed outlier: 6.076A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.657A pdb=" N SER E 56 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER E 32 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU E 81 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU E 123 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU E 83 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 166 through 167 removed outlier: 4.039A pdb=" N ARG A 166 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 172 through 173 removed outlier: 3.502A pdb=" N GLY A 172 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 69 through 72 Processing sheet with id=AF5, first strand: chain 'B' and resid 168 through 170 removed outlier: 4.063A pdb=" N LEU B 168 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.542A pdb=" N THR C 42 " --> pdb=" O PHE C 20 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 247 through 249 removed outlier: 3.533A pdb=" N LYS D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 260 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 265 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 316 through 324 removed outlier: 4.001A pdb=" N LEU E 413 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 520 through 521 Processing sheet with id=AG1, first strand: chain 'F' and resid 491 through 497 removed outlier: 7.061A pdb=" N VAL F 502 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N MET F 496 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY F 500 " --> pdb=" O MET F 496 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER F 503 " --> pdb=" O THR F 514 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 505 " --> pdb=" O SER F 512 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR F 511 " --> pdb=" O ASP F 530 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR F 526 " --> pdb=" O VAL F 515 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 536 through 539 Processing sheet with id=AG3, first strand: chain 'F' and resid 580 through 583 Processing sheet with id=AG4, first strand: chain 'F' and resid 615 through 620 removed outlier: 4.567A pdb=" N ILE F 615 " --> pdb=" O TYR F 630 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR F 630 " --> pdb=" O ILE F 615 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA F 617 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL F 628 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU F 640 " --> pdb=" O ARG F 653 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ARG F 653 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLU F 642 " --> pdb=" O TYR F 651 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR F 651 " --> pdb=" O GLU F 642 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 686 through 689 removed outlier: 3.771A pdb=" N LEU F 707 " --> pdb=" O PRO F 695 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 740 through 747 removed outlier: 3.876A pdb=" N HIS F 741 " --> pdb=" O VAL F 757 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 745 " --> pdb=" O ASN F 753 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN F 753 " --> pdb=" O LEU F 745 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU F 747 " --> pdb=" O THR F 751 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR F 751 " --> pdb=" O LEU F 747 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 491 through 496 removed outlier: 7.241A pdb=" N VAL G 502 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N MET G 496 " --> pdb=" O GLY G 500 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY G 500 " --> pdb=" O MET G 496 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 536 through 540 Processing sheet with id=AG9, first strand: chain 'G' and resid 580 through 583 removed outlier: 3.792A pdb=" N ARG G 598 " --> pdb=" O VAL G 590 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN G 601 " --> pdb=" O PRO G 606 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 617 through 620 removed outlier: 6.895A pdb=" N LEU G 640 " --> pdb=" O ARG G 653 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ARG G 653 " --> pdb=" O LEU G 640 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLU G 642 " --> pdb=" O TYR G 651 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR G 651 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 696 through 698 removed outlier: 6.821A pdb=" N LEU G 704 " --> pdb=" O ILE G 721 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 740 through 747 removed outlier: 7.294A pdb=" N ASN G 753 " --> pdb=" O LEU G 745 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU G 747 " --> pdb=" O THR G 751 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR G 751 " --> pdb=" O LEU G 747 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET G 774 " --> pdb=" O LEU G 752 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 491 through 496 removed outlier: 6.995A pdb=" N VAL H 502 " --> pdb=" O LEU H 494 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR H 511 " --> pdb=" O ASP H 530 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 515 " --> pdb=" O TYR H 526 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 536 through 540 Processing sheet with id=AH6, first strand: chain 'H' and resid 580 through 583 removed outlier: 3.572A pdb=" N ARG H 598 " --> pdb=" O VAL H 590 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 608 " --> pdb=" O SER H 599 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 615 through 620 removed outlier: 4.849A pdb=" N ILE H 615 " --> pdb=" O TYR H 630 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR H 630 " --> pdb=" O ILE H 615 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 617 " --> pdb=" O VAL H 628 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 628 " --> pdb=" O ALA H 617 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 641 through 642 Processing sheet with id=AH9, first strand: chain 'H' and resid 686 through 689 removed outlier: 4.242A pdb=" N LEU H 707 " --> pdb=" O PRO H 695 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 740 through 747 removed outlier: 7.366A pdb=" N ASN H 753 " --> pdb=" O LEU H 745 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU H 747 " --> pdb=" O THR H 751 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR H 751 " --> pdb=" O LEU H 747 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 1322 through 1327 removed outlier: 4.377A pdb=" N VAL M1324 " --> pdb=" O PHE M1339 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN M1326 " --> pdb=" O GLU M1337 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU M1336 " --> pdb=" O PHE M1351 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE M1351 " --> pdb=" O LEU M1336 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL M1338 " --> pdb=" O ILE M1349 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE M1349 " --> pdb=" O VAL M1338 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 1721 through 1722 removed outlier: 7.054A pdb=" N LEU M1867 " --> pdb=" O VAL M1859 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN M1729 " --> pdb=" O THR M1870 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 1726 through 1727 removed outlier: 3.782A pdb=" N TYR M1727 " --> pdb=" O LEU M1909 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU M1909 " --> pdb=" O TYR M1727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'M' and resid 2102 through 2107 removed outlier: 6.328A pdb=" N ILE M2117 " --> pdb=" O PRO M2104 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 171 through 173 removed outlier: 4.053A pdb=" N LYS N 171 " --> pdb=" O ALA N 533 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL N 540 " --> pdb=" O VAL N 640 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N CYS N 642 " --> pdb=" O VAL N 540 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE N 542 " --> pdb=" O CYS N 642 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET N 639 " --> pdb=" O ILE N 659 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 181 through 183 Processing sheet with id=AI8, first strand: chain 'N' and resid 304 through 307 removed outlier: 4.191A pdb=" N TRP N 296 " --> pdb=" O ILE N 307 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU N 327 " --> pdb=" O MET N 344 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N MET N 344 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU N 329 " --> pdb=" O THR N 342 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 523 through 525 removed outlier: 6.201A pdb=" N MET N 481 " --> pdb=" O VAL N 524 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE N 401 " --> pdb=" O MET N 673 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS N 681 " --> pdb=" O VAL N 676 " (cutoff:3.500A) 2873 hydrogen bonds defined for protein. 8298 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: 25.52 Time building geometry restraints manager: 15.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 20982 1.36 - 1.50: 16916 1.50 - 1.65: 26368 1.65 - 1.80: 280 1.80 - 1.95: 176 Bond restraints: 64722 Sorted by residual: bond pdb=" N PRO 5 525 " pdb=" CD PRO 5 525 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.14e+01 bond pdb=" C4 ADP 31001 " pdb=" C5 ADP 31001 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP 2 902 " pdb=" C5 ADP 2 902 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C GLY A 61 " pdb=" O GLY A 61 " ideal model delta sigma weight residual 1.235 1.306 -0.071 1.35e-02 5.49e+03 2.79e+01 bond pdb=" C LEU M1941 " pdb=" O LEU M1941 " ideal model delta sigma weight residual 1.236 1.303 -0.067 1.28e-02 6.10e+03 2.73e+01 ... (remaining 64717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 86743 2.99 - 5.97: 824 5.97 - 8.96: 81 8.96 - 11.94: 24 11.94 - 14.93: 3 Bond angle restraints: 87675 Sorted by residual: angle pdb=" CA GLN A 57 " pdb=" C GLN A 57 " pdb=" O GLN A 57 " ideal model delta sigma weight residual 121.07 114.81 6.26 1.10e+00 8.26e-01 3.24e+01 angle pdb=" N ILE F 762 " pdb=" CA ILE F 762 " pdb=" C ILE F 762 " ideal model delta sigma weight residual 111.91 107.32 4.59 8.90e-01 1.26e+00 2.66e+01 angle pdb=" C GLU 6 116 " pdb=" N GLN 6 117 " pdb=" CA GLN 6 117 " ideal model delta sigma weight residual 120.72 112.13 8.59 1.67e+00 3.59e-01 2.64e+01 angle pdb=" C HIS 7 620 " pdb=" N MET 7 621 " pdb=" CA MET 7 621 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C GLN 7 291 " pdb=" N ASN 7 292 " pdb=" CA ASN 7 292 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 ... (remaining 87670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.30: 38266 32.30 - 64.59: 1055 64.59 - 96.89: 107 96.89 - 129.18: 2 129.18 - 161.48: 3 Dihedral angle restraints: 39433 sinusoidal: 16226 harmonic: 23207 Sorted by residual: dihedral pdb=" C5' ADP 31001 " pdb=" O5' ADP 31001 " pdb=" PA ADP 31001 " pdb=" O2A ADP 31001 " ideal model delta sinusoidal sigma weight residual 300.00 138.53 161.48 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O1B ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PB ADP 31001 " pdb=" PA ADP 31001 " ideal model delta sinusoidal sigma weight residual 300.00 139.19 160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP 2 902 " pdb=" O5' ADP 2 902 " pdb=" PA ADP 2 902 " pdb=" O2A ADP 2 902 " ideal model delta sinusoidal sigma weight residual -60.00 72.64 -132.64 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 39430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 8055 0.055 - 0.109: 1610 0.109 - 0.163: 291 0.163 - 0.218: 38 0.218 - 0.272: 6 Chirality restraints: 10000 Sorted by residual: chirality pdb=" CB ILE G 615 " pdb=" CA ILE G 615 " pdb=" CG1 ILE G 615 " pdb=" CG2 ILE G 615 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PHE M1944 " pdb=" N PHE M1944 " pdb=" C PHE M1944 " pdb=" CB PHE M1944 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE 6 715 " pdb=" CA ILE 6 715 " pdb=" CG1 ILE 6 715 " pdb=" CG2 ILE 6 715 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 9997 not shown) Planarity restraints: 11151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN M1940 " 0.024 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C GLN M1940 " -0.082 2.00e-02 2.50e+03 pdb=" O GLN M1940 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU M1941 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 7 291 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C GLN 7 291 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN 7 291 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN 7 292 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 187 " 0.230 9.50e-02 1.11e+02 1.03e-01 6.53e+00 pdb=" NE ARG 6 187 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG 6 187 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 187 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 187 " 0.008 2.00e-02 2.50e+03 ... (remaining 11148 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 2 1.79 - 2.57: 1315 2.57 - 3.35: 97117 3.35 - 4.12: 179386 4.12 - 4.90: 304511 Nonbonded interactions: 582331 Sorted by model distance: nonbonded pdb=" ND2 ASN 3 312 " pdb=" O ASN 5 302 " model vdw 1.015 3.120 nonbonded pdb=" SD MET A 62 " pdb=" CB ALA A 68 " model vdw 1.699 3.820 nonbonded pdb=" OG SER 5 423 " pdb="MG MG 5 804 " model vdw 2.012 2.170 nonbonded pdb=" OH TYR 3 38 " pdb=" OD2 ASP 3 102 " model vdw 2.036 3.040 nonbonded pdb=" OG SER D 176 " pdb=" OD1 ASP D 178 " model vdw 2.049 3.040 ... (remaining 582326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 474 through 663 or resid 670 through 789 or (resid 790 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 892 o \ r (resid 893 through 894 and (name N or name CA or name C or name O or name CB ) \ ) or resid 895 through 901 or (resid 902 and (name N or name CA or name C or nam \ e O or name CB )) or resid 903 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 923)) selection = (chain 'G' and (resid 474 through 789 or (resid 790 and (name N or name CA or na \ me C or name O or name CB )) or resid 814 through 901 or (resid 902 and (name N \ or name CA or name C or name O or name CB )) or resid 903 through 909 or (resid \ 910 and (name N or name CA or name C or name O or name CB )) or resid 911 throug \ h 923)) selection = (chain 'H' and (resid 474 through 663 or resid 670 through 892 or (resid 893 thr \ ough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 t \ hrough 909 or (resid 910 and (name N or name CA or name C or name O or name CB ) \ ) or resid 911 or (resid 912 and (name N or name CA or name C or name O or name \ CB )) or resid 913 through 923)) } 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: 5.630 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: 0.050 Extract box with map and model: 2.040 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 120.000 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 64722 Z= 0.261 Angle : 0.772 14.925 87675 Z= 0.435 Chirality : 0.046 0.272 10000 Planarity : 0.005 0.103 11151 Dihedral : 14.795 161.476 24353 Min Nonbonded Distance : 1.015 Molprobity Statistics. All-atom Clashscore : 36.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.96 % Favored : 93.79 % Rotamer: Outliers : 0.74 % Allowed : 0.69 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.28 (0.09), residues: 7772 helix: 0.97 (0.09), residues: 3100 sheet: -0.66 (0.15), residues: 1142 loop : -1.04 (0.10), residues: 3530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 624 HIS 0.008 0.001 HIS 6 653 PHE 0.043 0.002 PHE 6 142 TYR 0.034 0.002 TYR 4 519 ARG 0.015 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 5.902 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: 2 267 MET cc_start: 0.9106 (ptp) cc_final: 0.8895 (ptp) REVERT: 2 783 MET cc_start: 0.9557 (mpp) cc_final: 0.8998 (tpt) REVERT: 2 788 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8864 (ptp-110) REVERT: 3 384 MET cc_start: 0.9077 (tpp) cc_final: 0.8828 (tpt) REVERT: 4 801 MET cc_start: 0.7158 (mmp) cc_final: 0.6829 (mmm) REVERT: 5 276 MET cc_start: 0.9402 (mpp) cc_final: 0.8818 (mpp) REVERT: 5 393 MET cc_start: 0.8108 (tpt) cc_final: 0.7518 (tpt) REVERT: 5 404 MET cc_start: 0.8608 (mmt) cc_final: 0.8080 (mmm) REVERT: 6 551 MET cc_start: 0.9417 (mmp) cc_final: 0.9148 (mmm) REVERT: 6 706 MET cc_start: 0.9077 (ppp) cc_final: 0.8856 (ppp) REVERT: 7 541 MET cc_start: 0.9554 (ppp) cc_final: 0.9243 (ppp) REVERT: A 58 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.6104 (tm-30) REVERT: A 75 THR cc_start: 0.9863 (OUTLIER) cc_final: 0.9622 (p) REVERT: A 79 MET cc_start: 0.9814 (ptp) cc_final: 0.9578 (ptp) REVERT: A 100 MET cc_start: 0.9718 (mmp) cc_final: 0.9511 (mmm) REVERT: B 189 MET cc_start: 0.9111 (tpt) cc_final: 0.8058 (tpt) REVERT: C 79 MET cc_start: 0.9240 (tpt) cc_final: 0.8996 (tpp) REVERT: D 129 MET cc_start: 0.9392 (mtt) cc_final: 0.9019 (tpp) REVERT: E 44 MET cc_start: 0.9465 (mmt) cc_final: 0.9236 (mmm) REVERT: F 726 MET cc_start: 0.9523 (tpt) cc_final: 0.9212 (tpt) REVERT: F 774 MET cc_start: 0.9547 (mmp) cc_final: 0.9343 (mmm) REVERT: F 821 MET cc_start: 0.9322 (tpt) cc_final: 0.8878 (tpt) REVERT: G 778 MET cc_start: 0.8218 (mpp) cc_final: 0.6942 (pmm) REVERT: H 496 MET cc_start: 0.9522 (mpp) cc_final: 0.9298 (mpp) REVERT: H 659 MET cc_start: 0.7226 (ppp) cc_final: 0.7015 (ppp) REVERT: M 1894 MET cc_start: 0.8550 (pmm) cc_final: 0.7901 (ppp) REVERT: M 2012 MET cc_start: 0.7731 (ppp) cc_final: 0.7159 (ppp) outliers start: 52 outliers final: 20 residues processed: 229 average time/residue: 0.6056 time to fit residues: 242.5387 Evaluate side-chains 200 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 6.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 662 optimal weight: 50.0000 chunk 594 optimal weight: 0.8980 chunk 329 optimal weight: 3.9990 chunk 202 optimal weight: 0.5980 chunk 400 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 614 optimal weight: 10.0000 chunk 237 optimal weight: 30.0000 chunk 373 optimal weight: 4.9990 chunk 457 optimal weight: 10.0000 chunk 711 optimal weight: 30.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 248 HIS ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 641 GLN ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 269 GLN 3 312 ASN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 5 499 GLN 5 581 ASN 6 182 GLN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS ** 6 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 518 ASN ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN E 289 ASN ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 ASN G 629 HIS H 915 ASN ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1723 ASN M1849 ASN ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1975 ASN ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 64722 Z= 0.217 Angle : 0.677 11.290 87675 Z= 0.359 Chirality : 0.044 0.258 10000 Planarity : 0.005 0.062 11151 Dihedral : 8.565 158.080 8872 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.70 % Favored : 94.17 % Rotamer: Outliers : 0.16 % Allowed : 6.47 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.33 (0.09), residues: 7772 helix: 0.92 (0.09), residues: 3261 sheet: -0.76 (0.15), residues: 1111 loop : -1.12 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M1956 HIS 0.016 0.001 HIS 6 730 PHE 0.029 0.002 PHE 6 115 TYR 0.040 0.002 TYR 6 754 ARG 0.008 0.001 ARG 2 836 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 5.868 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: 2 267 MET cc_start: 0.9094 (ptp) cc_final: 0.8860 (ptp) REVERT: 3 136 MET cc_start: 0.8596 (tmm) cc_final: 0.8341 (tmm) REVERT: 3 384 MET cc_start: 0.9026 (tpp) cc_final: 0.8807 (tpt) REVERT: 4 801 MET cc_start: 0.7060 (mmp) cc_final: 0.6705 (mmm) REVERT: 5 276 MET cc_start: 0.9259 (mpp) cc_final: 0.8845 (mpp) REVERT: 5 393 MET cc_start: 0.8298 (tpt) cc_final: 0.7863 (tpt) REVERT: 5 404 MET cc_start: 0.8162 (mmt) cc_final: 0.7734 (mmm) REVERT: 6 551 MET cc_start: 0.9488 (mmp) cc_final: 0.9193 (mmm) REVERT: 6 644 MET cc_start: 0.7952 (mmt) cc_final: 0.7395 (mmt) REVERT: 6 706 MET cc_start: 0.9165 (ppp) cc_final: 0.8868 (ppp) REVERT: 7 541 MET cc_start: 0.9691 (ppp) cc_final: 0.9361 (ppp) REVERT: B 189 MET cc_start: 0.9142 (tpt) cc_final: 0.8122 (tpt) REVERT: C 79 MET cc_start: 0.9277 (tpt) cc_final: 0.8924 (tpp) REVERT: D 129 MET cc_start: 0.9413 (mtt) cc_final: 0.9026 (tpp) REVERT: E 44 MET cc_start: 0.9344 (mmt) cc_final: 0.9138 (mmm) REVERT: F 659 MET cc_start: 0.8907 (tmm) cc_final: 0.8672 (tmm) REVERT: F 726 MET cc_start: 0.9547 (tpt) cc_final: 0.9174 (tpt) REVERT: F 821 MET cc_start: 0.9320 (tpt) cc_final: 0.8863 (tpp) REVERT: G 778 MET cc_start: 0.8298 (mpp) cc_final: 0.6944 (pmm) REVERT: M 1957 MET cc_start: 0.8599 (ppp) cc_final: 0.8253 (ppp) outliers start: 11 outliers final: 4 residues processed: 193 average time/residue: 0.5509 time to fit residues: 193.3473 Evaluate side-chains 182 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 5.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 395 optimal weight: 0.9980 chunk 220 optimal weight: 7.9990 chunk 592 optimal weight: 30.0000 chunk 484 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 713 optimal weight: 5.9990 chunk 770 optimal weight: 4.9990 chunk 635 optimal weight: 6.9990 chunk 707 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 572 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 576 GLN ** 4 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 5 24 ASN ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 344 ASN 5 499 GLN 5 581 ASN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 107 GLN A 18 GLN A 50 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 ASN ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 891 GLN ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 64722 Z= 0.230 Angle : 0.663 13.075 87675 Z= 0.350 Chirality : 0.044 0.219 10000 Planarity : 0.005 0.074 11151 Dihedral : 8.526 158.612 8872 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 27.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.69 % Favored : 94.17 % Rotamer: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.36 (0.09), residues: 7772 helix: 0.93 (0.09), residues: 3261 sheet: -0.86 (0.15), residues: 1115 loop : -1.13 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M1956 HIS 0.013 0.001 HIS 6 730 PHE 0.031 0.002 PHE 7 355 TYR 0.034 0.002 TYR 6 754 ARG 0.017 0.001 ARG G 649 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 7.325 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: 2 267 MET cc_start: 0.9177 (ptp) cc_final: 0.8956 (ptp) REVERT: 2 783 MET cc_start: 0.9549 (mpp) cc_final: 0.9035 (tpp) REVERT: 3 136 MET cc_start: 0.8601 (tmm) cc_final: 0.8295 (tmm) REVERT: 4 801 MET cc_start: 0.6883 (mmp) cc_final: 0.6564 (mmm) REVERT: 5 276 MET cc_start: 0.9293 (mpp) cc_final: 0.8826 (mpp) REVERT: 5 393 MET cc_start: 0.8206 (tpt) cc_final: 0.7739 (tpp) REVERT: 5 404 MET cc_start: 0.8206 (mmt) cc_final: 0.7781 (mmm) REVERT: 6 551 MET cc_start: 0.9555 (mmp) cc_final: 0.9310 (mmm) REVERT: 6 644 MET cc_start: 0.7891 (mmt) cc_final: 0.7446 (mmt) REVERT: 6 706 MET cc_start: 0.9155 (ppp) cc_final: 0.8833 (ppp) REVERT: 7 541 MET cc_start: 0.9706 (ppp) cc_final: 0.9385 (ppp) REVERT: B 189 MET cc_start: 0.9301 (tpt) cc_final: 0.8170 (tpt) REVERT: C 79 MET cc_start: 0.9330 (tpt) cc_final: 0.8926 (tpp) REVERT: D 129 MET cc_start: 0.9415 (mtt) cc_final: 0.9047 (tpp) REVERT: E 44 MET cc_start: 0.9411 (mmt) cc_final: 0.9152 (mmm) REVERT: F 659 MET cc_start: 0.8824 (tmm) cc_final: 0.8518 (tmm) REVERT: F 726 MET cc_start: 0.9569 (tpt) cc_final: 0.9177 (tpp) REVERT: F 821 MET cc_start: 0.9358 (tpt) cc_final: 0.8839 (tpt) REVERT: G 778 MET cc_start: 0.8224 (mpp) cc_final: 0.7610 (pmm) REVERT: M 1957 MET cc_start: 0.8622 (ppp) cc_final: 0.8282 (ppp) outliers start: 6 outliers final: 4 residues processed: 186 average time/residue: 0.5770 time to fit residues: 194.5534 Evaluate side-chains 182 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 704 optimal weight: 20.0000 chunk 536 optimal weight: 9.9990 chunk 370 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 340 optimal weight: 40.0000 chunk 478 optimal weight: 5.9990 chunk 715 optimal weight: 30.0000 chunk 757 optimal weight: 0.8980 chunk 373 optimal weight: 4.9990 chunk 678 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN ** 4 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 499 GLN 5 574 ASN 5 581 ASN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 550 GLN ** 6 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 209 GLN ** 7 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 554 ASN 7 622 HIS ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 HIS ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 761 HIS ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 64722 Z= 0.228 Angle : 0.662 10.990 87675 Z= 0.347 Chirality : 0.044 0.259 10000 Planarity : 0.005 0.070 11151 Dihedral : 8.512 155.675 8872 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 27.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.79 % Favored : 94.06 % Rotamer: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.40 (0.09), residues: 7772 helix: 0.92 (0.09), residues: 3270 sheet: -0.99 (0.15), residues: 1100 loop : -1.15 (0.11), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M1956 HIS 0.012 0.001 HIS 6 730 PHE 0.028 0.002 PHE N 458 TYR 0.039 0.002 TYR 4 226 ARG 0.013 0.001 ARG 2 836 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 5.989 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: 2 783 MET cc_start: 0.9575 (mpp) cc_final: 0.9032 (tpp) REVERT: 3 136 MET cc_start: 0.8763 (tmm) cc_final: 0.8422 (tmm) REVERT: 4 637 MET cc_start: 0.5079 (mmt) cc_final: 0.4485 (mmt) REVERT: 4 801 MET cc_start: 0.6971 (mmp) cc_final: 0.6670 (mmm) REVERT: 5 276 MET cc_start: 0.9270 (mpp) cc_final: 0.8788 (mpp) REVERT: 5 404 MET cc_start: 0.8139 (mmt) cc_final: 0.7743 (mmm) REVERT: 5 469 MET cc_start: 0.9786 (mpp) cc_final: 0.9274 (mmp) REVERT: 6 551 MET cc_start: 0.9565 (mmp) cc_final: 0.9325 (mmm) REVERT: 6 644 MET cc_start: 0.7920 (mmt) cc_final: 0.7627 (mmm) REVERT: 6 706 MET cc_start: 0.9159 (ppp) cc_final: 0.8840 (ppp) REVERT: 7 541 MET cc_start: 0.9715 (ppp) cc_final: 0.9394 (ppp) REVERT: B 189 MET cc_start: 0.9247 (tpt) cc_final: 0.8228 (tpt) REVERT: C 79 MET cc_start: 0.9358 (tpt) cc_final: 0.8879 (tpp) REVERT: D 129 MET cc_start: 0.9416 (mtt) cc_final: 0.9056 (tpp) REVERT: E 44 MET cc_start: 0.9444 (mmt) cc_final: 0.9163 (mmm) REVERT: F 659 MET cc_start: 0.8841 (tmm) cc_final: 0.8534 (tmm) REVERT: F 726 MET cc_start: 0.9549 (tpt) cc_final: 0.9094 (tpt) REVERT: F 821 MET cc_start: 0.9279 (tpt) cc_final: 0.8768 (tpt) REVERT: G 778 MET cc_start: 0.8382 (mpp) cc_final: 0.8137 (mpp) REVERT: M 1957 MET cc_start: 0.8580 (ppp) cc_final: 0.8296 (ppp) REVERT: M 2062 MET cc_start: 0.9204 (mtm) cc_final: 0.9002 (mtp) outliers start: 2 outliers final: 1 residues processed: 185 average time/residue: 0.5689 time to fit residues: 190.7125 Evaluate side-chains 180 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 631 optimal weight: 40.0000 chunk 430 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 564 optimal weight: 0.0870 chunk 312 optimal weight: 6.9990 chunk 646 optimal weight: 6.9990 chunk 523 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 386 optimal weight: 5.9990 chunk 680 optimal weight: 9.9990 chunk 191 optimal weight: 50.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 55 ASN ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN ** 4 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 334 GLN 5 499 GLN 5 581 ASN 5 676 HIS ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 514 ASN ** 6 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 916 ASN ** H 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M2022 GLN ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 64722 Z= 0.215 Angle : 0.658 13.482 87675 Z= 0.345 Chirality : 0.044 0.276 10000 Planarity : 0.005 0.060 11151 Dihedral : 8.504 155.267 8872 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.80 % Favored : 94.04 % Rotamer: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.40 (0.09), residues: 7772 helix: 0.94 (0.09), residues: 3286 sheet: -1.03 (0.15), residues: 1099 loop : -1.16 (0.11), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP M1956 HIS 0.009 0.001 HIS 6 730 PHE 0.030 0.002 PHE M1915 TYR 0.031 0.002 TYR E 103 ARG 0.014 0.001 ARG 6 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 6.301 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: 2 267 MET cc_start: 0.9198 (ptp) cc_final: 0.8917 (ptp) REVERT: 3 136 MET cc_start: 0.8829 (tmm) cc_final: 0.8496 (tmm) REVERT: 4 637 MET cc_start: 0.5078 (mmt) cc_final: 0.4543 (mmt) REVERT: 4 801 MET cc_start: 0.7069 (mmp) cc_final: 0.6823 (mmm) REVERT: 5 276 MET cc_start: 0.9293 (mpp) cc_final: 0.8950 (mpp) REVERT: 5 393 MET cc_start: 0.8226 (tpt) cc_final: 0.7804 (tpp) REVERT: 5 404 MET cc_start: 0.7928 (mmt) cc_final: 0.7569 (mmm) REVERT: 5 469 MET cc_start: 0.9786 (mpp) cc_final: 0.9276 (mmp) REVERT: 5 599 MET cc_start: 0.9591 (mtt) cc_final: 0.9302 (mtt) REVERT: 6 551 MET cc_start: 0.9577 (mmp) cc_final: 0.9344 (mmm) REVERT: 6 644 MET cc_start: 0.7928 (mmt) cc_final: 0.7630 (mmm) REVERT: 6 706 MET cc_start: 0.9168 (ppp) cc_final: 0.8841 (ppp) REVERT: 7 506 MET cc_start: 0.4465 (mmp) cc_final: 0.4225 (mmp) REVERT: 7 541 MET cc_start: 0.9720 (ppp) cc_final: 0.9393 (ppp) REVERT: B 189 MET cc_start: 0.9245 (tpt) cc_final: 0.8091 (tpt) REVERT: C 79 MET cc_start: 0.9377 (tpt) cc_final: 0.8856 (tpp) REVERT: D 129 MET cc_start: 0.9414 (mtt) cc_final: 0.9055 (tpp) REVERT: E 44 MET cc_start: 0.9462 (mmt) cc_final: 0.9171 (mmm) REVERT: F 659 MET cc_start: 0.8836 (tmm) cc_final: 0.8448 (tmm) REVERT: F 726 MET cc_start: 0.9551 (tpt) cc_final: 0.9076 (tpt) REVERT: F 821 MET cc_start: 0.9316 (tpt) cc_final: 0.8807 (tpt) REVERT: G 778 MET cc_start: 0.8351 (mpp) cc_final: 0.8082 (mpp) REVERT: G 847 MET cc_start: 0.8327 (ptt) cc_final: 0.7936 (pmm) REVERT: M 1957 MET cc_start: 0.8362 (ppp) cc_final: 0.8042 (ppp) outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.5820 time to fit residues: 193.3911 Evaluate side-chains 180 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 6.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 254 optimal weight: 8.9990 chunk 682 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 444 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 758 optimal weight: 0.0980 chunk 629 optimal weight: 0.9990 chunk 351 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 398 optimal weight: 8.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 405 HIS ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 239 ASN ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 4 757 HIS ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 499 GLN 5 581 ASN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 64722 Z= 0.204 Angle : 0.649 12.903 87675 Z= 0.340 Chirality : 0.044 0.233 10000 Planarity : 0.005 0.071 11151 Dihedral : 8.495 155.965 8872 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.37 (0.10), residues: 7772 helix: 0.98 (0.09), residues: 3281 sheet: -1.06 (0.15), residues: 1113 loop : -1.15 (0.11), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP M1956 HIS 0.009 0.001 HIS G 629 PHE 0.034 0.002 PHE A 189 TYR 0.045 0.002 TYR 4 519 ARG 0.016 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 6.117 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: 2 267 MET cc_start: 0.9189 (ptp) cc_final: 0.8904 (ptp) REVERT: 3 136 MET cc_start: 0.8797 (tmm) cc_final: 0.8452 (tmm) REVERT: 4 637 MET cc_start: 0.4979 (mmt) cc_final: 0.4476 (mmt) REVERT: 5 276 MET cc_start: 0.9283 (mpp) cc_final: 0.8951 (mpp) REVERT: 5 393 MET cc_start: 0.8229 (tpt) cc_final: 0.7796 (tpp) REVERT: 5 404 MET cc_start: 0.7690 (mmt) cc_final: 0.7401 (mmm) REVERT: 5 469 MET cc_start: 0.9802 (mpp) cc_final: 0.9289 (mmp) REVERT: 6 551 MET cc_start: 0.9588 (mmp) cc_final: 0.9353 (mmm) REVERT: 6 644 MET cc_start: 0.7920 (mmt) cc_final: 0.7615 (mmm) REVERT: 7 529 MET cc_start: 0.8624 (ppp) cc_final: 0.7503 (ppp) REVERT: 7 541 MET cc_start: 0.9725 (ppp) cc_final: 0.9393 (ppp) REVERT: 7 652 MET cc_start: 0.6423 (ppp) cc_final: 0.6104 (ppp) REVERT: A 100 MET cc_start: 0.9703 (mmp) cc_final: 0.9485 (mmm) REVERT: B 189 MET cc_start: 0.9235 (tpt) cc_final: 0.8076 (tpt) REVERT: C 79 MET cc_start: 0.9380 (tpt) cc_final: 0.8799 (tpp) REVERT: E 44 MET cc_start: 0.9448 (mmt) cc_final: 0.9110 (mmm) REVERT: F 659 MET cc_start: 0.8798 (tmm) cc_final: 0.8408 (tmm) REVERT: F 726 MET cc_start: 0.9546 (tpt) cc_final: 0.9046 (tpt) REVERT: F 821 MET cc_start: 0.9353 (tpt) cc_final: 0.8840 (tpt) REVERT: G 778 MET cc_start: 0.8375 (mpp) cc_final: 0.8138 (mpp) REVERT: G 847 MET cc_start: 0.8473 (ptt) cc_final: 0.8092 (pmm) REVERT: H 496 MET cc_start: 0.9611 (mpp) cc_final: 0.9410 (mpp) REVERT: M 1957 MET cc_start: 0.8359 (ppp) cc_final: 0.8059 (ppp) outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.5696 time to fit residues: 189.3809 Evaluate side-chains 180 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 5.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 731 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 432 optimal weight: 20.0000 chunk 553 optimal weight: 4.9990 chunk 429 optimal weight: 20.0000 chunk 638 optimal weight: 7.9990 chunk 423 optimal weight: 6.9990 chunk 755 optimal weight: 50.0000 chunk 472 optimal weight: 2.9990 chunk 460 optimal weight: 7.9990 chunk 348 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 239 ASN ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 492 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 549 ASN 4 691 ASN ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 895 GLN 5 499 GLN 5 581 ASN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 HIS ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 753 ASN ** H 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M2178 HIS ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 64722 Z= 0.239 Angle : 0.672 12.444 87675 Z= 0.353 Chirality : 0.044 0.302 10000 Planarity : 0.005 0.062 11151 Dihedral : 8.529 154.910 8872 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.06 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.43 (0.10), residues: 7772 helix: 0.94 (0.09), residues: 3264 sheet: -1.06 (0.15), residues: 1121 loop : -1.18 (0.11), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M1956 HIS 0.008 0.001 HIS G 629 PHE 0.028 0.002 PHE A 189 TYR 0.038 0.002 TYR 4 519 ARG 0.017 0.001 ARG 6 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 6.104 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: 2 267 MET cc_start: 0.9213 (ptp) cc_final: 0.8957 (ptp) REVERT: 3 136 MET cc_start: 0.8767 (tmm) cc_final: 0.8426 (tmm) REVERT: 4 637 MET cc_start: 0.5050 (mmt) cc_final: 0.4490 (mmt) REVERT: 5 276 MET cc_start: 0.9256 (mpp) cc_final: 0.8991 (mpp) REVERT: 5 404 MET cc_start: 0.7877 (mmt) cc_final: 0.7551 (mmm) REVERT: 6 551 MET cc_start: 0.9632 (mmp) cc_final: 0.9396 (mmm) REVERT: 6 644 MET cc_start: 0.7981 (mmt) cc_final: 0.7437 (mmt) REVERT: 6 706 MET cc_start: 0.9171 (ppp) cc_final: 0.8858 (ppp) REVERT: 7 506 MET cc_start: 0.4769 (mmp) cc_final: 0.4511 (mmp) REVERT: 7 541 MET cc_start: 0.9730 (ppp) cc_final: 0.9380 (ppp) REVERT: 7 652 MET cc_start: 0.6557 (ppp) cc_final: 0.6181 (ppp) REVERT: A 100 MET cc_start: 0.9707 (mmp) cc_final: 0.9501 (mmm) REVERT: B 189 MET cc_start: 0.9260 (tpt) cc_final: 0.8087 (tpt) REVERT: C 79 MET cc_start: 0.9399 (tpt) cc_final: 0.8783 (tpp) REVERT: D 129 MET cc_start: 0.9355 (mtt) cc_final: 0.8838 (mmt) REVERT: E 44 MET cc_start: 0.9452 (mmt) cc_final: 0.9091 (mmm) REVERT: F 659 MET cc_start: 0.8765 (tmm) cc_final: 0.8357 (tmm) REVERT: F 726 MET cc_start: 0.9538 (tpt) cc_final: 0.9031 (tpt) REVERT: F 821 MET cc_start: 0.9282 (tpt) cc_final: 0.8653 (tpt) REVERT: G 778 MET cc_start: 0.8372 (mpp) cc_final: 0.8121 (mpp) REVERT: G 847 MET cc_start: 0.8491 (ptt) cc_final: 0.8130 (pmm) REVERT: H 659 MET cc_start: 0.7135 (ppp) cc_final: 0.6892 (ppp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5890 time to fit residues: 192.2949 Evaluate side-chains 179 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 467 optimal weight: 0.9980 chunk 301 optimal weight: 7.9990 chunk 451 optimal weight: 10.0000 chunk 227 optimal weight: 0.0370 chunk 148 optimal weight: 40.0000 chunk 146 optimal weight: 8.9990 chunk 480 optimal weight: 5.9990 chunk 514 optimal weight: 0.9990 chunk 373 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 593 optimal weight: 10.0000 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 499 GLN 5 581 ASN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 833 GLN ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 64722 Z= 0.193 Angle : 0.659 11.967 87675 Z= 0.344 Chirality : 0.044 0.273 10000 Planarity : 0.005 0.130 11151 Dihedral : 8.513 158.100 8872 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.37 (0.10), residues: 7772 helix: 0.99 (0.09), residues: 3260 sheet: -1.01 (0.15), residues: 1095 loop : -1.17 (0.11), residues: 3417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M1956 HIS 0.007 0.001 HIS 6 730 PHE 0.024 0.002 PHE A 189 TYR 0.036 0.002 TYR 4 519 ARG 0.017 0.001 ARG 2 836 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 6.695 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: 3 136 MET cc_start: 0.8819 (tmm) cc_final: 0.8510 (tmm) REVERT: 4 637 MET cc_start: 0.5116 (mmt) cc_final: 0.4558 (mmt) REVERT: 4 801 MET cc_start: 0.6573 (mmm) cc_final: 0.6139 (mmm) REVERT: 5 276 MET cc_start: 0.9270 (mpp) cc_final: 0.8996 (mpp) REVERT: 5 348 MET cc_start: 0.8726 (mmp) cc_final: 0.8517 (mmm) REVERT: 5 404 MET cc_start: 0.7265 (mmt) cc_final: 0.7065 (mmm) REVERT: 6 551 MET cc_start: 0.9630 (mmp) cc_final: 0.9377 (mmm) REVERT: 6 644 MET cc_start: 0.7904 (mmt) cc_final: 0.7333 (mmt) REVERT: 6 706 MET cc_start: 0.9183 (ppp) cc_final: 0.8859 (ppp) REVERT: 7 506 MET cc_start: 0.4767 (mmp) cc_final: 0.4495 (mmp) REVERT: 7 529 MET cc_start: 0.8450 (ppp) cc_final: 0.7266 (ppp) REVERT: 7 541 MET cc_start: 0.9703 (ppp) cc_final: 0.9329 (ppp) REVERT: 7 652 MET cc_start: 0.6609 (ppp) cc_final: 0.6189 (ppp) REVERT: A 100 MET cc_start: 0.9703 (mmp) cc_final: 0.9490 (mmm) REVERT: B 189 MET cc_start: 0.9226 (tpt) cc_final: 0.8129 (tpt) REVERT: C 79 MET cc_start: 0.9382 (tpt) cc_final: 0.8771 (tpp) REVERT: D 129 MET cc_start: 0.9330 (mtt) cc_final: 0.8823 (mmt) REVERT: D 218 MET cc_start: 0.8948 (ptp) cc_final: 0.8665 (pmm) REVERT: E 44 MET cc_start: 0.9280 (mmt) cc_final: 0.8961 (mmm) REVERT: F 659 MET cc_start: 0.8800 (tmm) cc_final: 0.8377 (tmm) REVERT: F 726 MET cc_start: 0.9530 (tpt) cc_final: 0.9010 (tpt) REVERT: F 821 MET cc_start: 0.9335 (tpt) cc_final: 0.8731 (tpt) REVERT: G 778 MET cc_start: 0.8263 (mpp) cc_final: 0.8044 (mpp) REVERT: G 847 MET cc_start: 0.8562 (ptt) cc_final: 0.8265 (pmm) REVERT: H 496 MET cc_start: 0.9601 (mpp) cc_final: 0.9392 (mpp) REVERT: H 659 MET cc_start: 0.7429 (ppp) cc_final: 0.7217 (ppp) REVERT: M 1482 MET cc_start: 0.5151 (ttt) cc_final: 0.4772 (tpt) REVERT: M 1957 MET cc_start: 0.8418 (ppp) cc_final: 0.8215 (ppp) REVERT: M 2062 MET cc_start: 0.9141 (mtm) cc_final: 0.8815 (ptm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.5701 time to fit residues: 188.3319 Evaluate side-chains 179 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 6.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 687 optimal weight: 10.0000 chunk 723 optimal weight: 9.9990 chunk 660 optimal weight: 20.0000 chunk 704 optimal weight: 30.0000 chunk 423 optimal weight: 0.5980 chunk 306 optimal weight: 7.9990 chunk 552 optimal weight: 5.9990 chunk 216 optimal weight: 0.0870 chunk 636 optimal weight: 5.9990 chunk 665 optimal weight: 30.0000 chunk 701 optimal weight: 9.9990 overall best weight: 4.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 581 ASN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 891 GLN ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1534 GLN M1975 ASN ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 64722 Z= 0.210 Angle : 0.666 11.923 87675 Z= 0.349 Chirality : 0.044 0.242 10000 Planarity : 0.005 0.103 11151 Dihedral : 8.483 153.208 8872 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.88 % Favored : 93.97 % Rotamer: Outliers : 0.01 % Allowed : 0.89 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.37 (0.10), residues: 7772 helix: 1.00 (0.09), residues: 3270 sheet: -0.95 (0.15), residues: 1090 loop : -1.20 (0.11), residues: 3412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M1956 HIS 0.006 0.001 HIS H 629 PHE 0.030 0.002 PHE 7 24 TYR 0.034 0.002 TYR 4 519 ARG 0.013 0.001 ARG G 649 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 6.098 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: 3 136 MET cc_start: 0.8806 (tmm) cc_final: 0.8496 (tmm) REVERT: 3 407 MET cc_start: 0.9508 (tmm) cc_final: 0.9221 (tmm) REVERT: 4 637 MET cc_start: 0.5040 (mmt) cc_final: 0.4479 (mmt) REVERT: 5 276 MET cc_start: 0.9264 (mpp) cc_final: 0.8998 (mpp) REVERT: 5 348 MET cc_start: 0.8725 (mmp) cc_final: 0.8503 (mmm) REVERT: 5 393 MET cc_start: 0.8072 (tpt) cc_final: 0.7686 (tpt) REVERT: 5 404 MET cc_start: 0.7337 (mmt) cc_final: 0.7122 (mmm) REVERT: 6 551 MET cc_start: 0.9630 (mmp) cc_final: 0.9372 (mmm) REVERT: 6 644 MET cc_start: 0.7938 (mmt) cc_final: 0.7345 (mmt) REVERT: 6 706 MET cc_start: 0.9188 (ppp) cc_final: 0.8877 (ppp) REVERT: 7 529 MET cc_start: 0.8468 (ppp) cc_final: 0.7314 (ppp) REVERT: 7 541 MET cc_start: 0.9702 (ppp) cc_final: 0.9323 (ppp) REVERT: A 100 MET cc_start: 0.9708 (mmp) cc_final: 0.9498 (mmm) REVERT: B 189 MET cc_start: 0.9237 (tpt) cc_final: 0.8126 (tpt) REVERT: C 79 MET cc_start: 0.9394 (tpt) cc_final: 0.8750 (tpp) REVERT: D 129 MET cc_start: 0.9342 (mtt) cc_final: 0.8843 (mmt) REVERT: D 218 MET cc_start: 0.8962 (ptp) cc_final: 0.8464 (pmm) REVERT: E 44 MET cc_start: 0.9259 (mmt) cc_final: 0.8924 (mmm) REVERT: F 496 MET cc_start: 0.9464 (mmp) cc_final: 0.9241 (mmp) REVERT: F 659 MET cc_start: 0.8732 (tmm) cc_final: 0.8284 (tmm) REVERT: F 726 MET cc_start: 0.9466 (tpt) cc_final: 0.8994 (tpp) REVERT: F 821 MET cc_start: 0.9378 (tpt) cc_final: 0.8820 (tpt) REVERT: G 778 MET cc_start: 0.8255 (mpp) cc_final: 0.8024 (mpp) REVERT: G 847 MET cc_start: 0.8525 (ptt) cc_final: 0.8232 (pmm) REVERT: H 496 MET cc_start: 0.9580 (mpp) cc_final: 0.9366 (mpp) REVERT: H 659 MET cc_start: 0.7504 (ppp) cc_final: 0.7300 (ppp) REVERT: M 1482 MET cc_start: 0.5201 (ttt) cc_final: 0.4792 (tpt) REVERT: M 1957 MET cc_start: 0.8416 (ppp) cc_final: 0.8207 (ppp) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.5955 time to fit residues: 195.6760 Evaluate side-chains 179 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 5.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 462 optimal weight: 2.9990 chunk 744 optimal weight: 8.9990 chunk 454 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 517 optimal weight: 6.9990 chunk 781 optimal weight: 0.5980 chunk 718 optimal weight: 0.1980 chunk 621 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 480 optimal weight: 0.8980 chunk 381 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 210 HIS ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 4 823 GLN 5 581 ASN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 833 GLN A 18 GLN B 128 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 64722 Z= 0.177 Angle : 0.673 11.798 87675 Z= 0.348 Chirality : 0.044 0.236 10000 Planarity : 0.005 0.097 11151 Dihedral : 8.437 156.743 8872 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.42 % Favored : 94.43 % Rotamer: Outliers : 0.01 % Allowed : 0.62 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.31 (0.10), residues: 7772 helix: 1.05 (0.09), residues: 3262 sheet: -0.95 (0.15), residues: 1088 loop : -1.15 (0.11), residues: 3422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M1956 HIS 0.009 0.001 HIS 6 735 PHE 0.028 0.001 PHE 7 24 TYR 0.033 0.002 TYR 4 519 ARG 0.018 0.001 ARG 3 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 6.011 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: 2 267 MET cc_start: 0.9171 (ptp) cc_final: 0.8881 (ptp) REVERT: 3 136 MET cc_start: 0.8830 (tmm) cc_final: 0.8512 (tmm) REVERT: 4 637 MET cc_start: 0.5030 (mmt) cc_final: 0.4525 (mmt) REVERT: 5 276 MET cc_start: 0.9310 (mpp) cc_final: 0.8943 (mpp) REVERT: 6 551 MET cc_start: 0.9598 (mmp) cc_final: 0.9339 (mmm) REVERT: 6 644 MET cc_start: 0.7871 (mmt) cc_final: 0.7311 (mmt) REVERT: 6 706 MET cc_start: 0.9233 (ppp) cc_final: 0.8901 (ppp) REVERT: 7 529 MET cc_start: 0.8458 (ppp) cc_final: 0.7247 (ppp) REVERT: 7 541 MET cc_start: 0.9687 (ppp) cc_final: 0.9298 (ppp) REVERT: A 100 MET cc_start: 0.9709 (mmp) cc_final: 0.9472 (mmm) REVERT: B 189 MET cc_start: 0.9182 (tpt) cc_final: 0.7985 (tpt) REVERT: C 79 MET cc_start: 0.9364 (tpt) cc_final: 0.8454 (tpp) REVERT: D 218 MET cc_start: 0.9012 (ptp) cc_final: 0.8502 (pmm) REVERT: E 44 MET cc_start: 0.9214 (mmt) cc_final: 0.8874 (mmm) REVERT: F 726 MET cc_start: 0.9471 (tpt) cc_final: 0.8968 (tpp) REVERT: F 774 MET cc_start: 0.9639 (mmp) cc_final: 0.9398 (mmm) REVERT: F 821 MET cc_start: 0.9379 (tpt) cc_final: 0.8804 (tpt) REVERT: G 778 MET cc_start: 0.8275 (mpp) cc_final: 0.8043 (mpp) REVERT: G 847 MET cc_start: 0.8704 (ptt) cc_final: 0.8417 (pmm) REVERT: H 496 MET cc_start: 0.9563 (mpp) cc_final: 0.9347 (mpp) REVERT: H 659 MET cc_start: 0.7538 (ppp) cc_final: 0.7306 (ppp) REVERT: M 1482 MET cc_start: 0.5218 (ttt) cc_final: 0.4811 (tpt) REVERT: M 1957 MET cc_start: 0.8319 (ppp) cc_final: 0.8048 (ppp) REVERT: M 2062 MET cc_start: 0.9124 (mtm) cc_final: 0.8895 (ptm) outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.5782 time to fit residues: 192.8076 Evaluate side-chains 181 residues out of total 7102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 5.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 494 optimal weight: 9.9990 chunk 662 optimal weight: 40.0000 chunk 190 optimal weight: 9.9990 chunk 573 optimal weight: 20.0000 chunk 91 optimal weight: 0.0170 chunk 172 optimal weight: 6.9990 chunk 622 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 639 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 184 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 5 581 ASN ** 5 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 730 HIS ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.032624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.022645 restraints weight = 1132482.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.022889 restraints weight = 865275.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.023216 restraints weight = 673827.419| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 64722 Z= 0.210 Angle : 0.663 11.599 87675 Z= 0.346 Chirality : 0.044 0.243 10000 Planarity : 0.005 0.072 11151 Dihedral : 8.416 151.866 8872 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.83 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.31 (0.10), residues: 7772 helix: 1.07 (0.09), residues: 3271 sheet: -0.96 (0.15), residues: 1102 loop : -1.18 (0.11), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M1956 HIS 0.006 0.001 HIS H 629 PHE 0.022 0.002 PHE 6 115 TYR 0.032 0.002 TYR 4 519 ARG 0.016 0.001 ARG 6 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7964.78 seconds wall clock time: 146 minutes 47.44 seconds (8807.44 seconds total)