Starting phenix.real_space_refine on Fri Aug 9 08:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/08_2024/7ok0_12960.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/08_2024/7ok0_12960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/08_2024/7ok0_12960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/08_2024/7ok0_12960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/08_2024/7ok0_12960.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ok0_12960/08_2024/7ok0_12960.cif" } resolution = 2.9 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= -0.000 sd= 1.000 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 Fe 3 7.16 5 Zn 6 6.06 5 Mg 1 5.21 5 S 122 5.16 5 C 16294 2.51 5 N 4427 2.21 5 O 4783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "B GLU 841": "OE1" <-> "OE2" Residue "B ASP 846": "OD1" <-> "OD2" Residue "B ASP 998": "OD1" <-> "OD2" Residue "B ASP 1033": "OD1" <-> "OD2" Residue "B TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ASP 49": "OD1" <-> "OD2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G ASP 67": "OD1" <-> "OD2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 43": "OD1" <-> "OD2" Residue "K ASP 51": "OD1" <-> "OD2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "P ASP 14": "OD1" <-> "OD2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "Q ASP 49": "OD1" <-> "OD2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25636 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 7023 Classifications: {'peptide': 880} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 827} 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: 8725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8725 Classifications: {'peptide': 1109} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1055} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3087 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 384} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2057 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 402 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 991 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 617 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 690 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "N" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 534 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "P" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 376 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 357 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'F3S': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 435 SG CYS A 58 18.367 75.532 45.318 1.00124.98 S ATOM 455 SG CYS A 61 18.421 71.740 44.766 1.00122.81 S ATOM 497 SG CYS A 68 20.583 73.306 47.472 1.00117.60 S ATOM 744 SG CYS A 98 54.448 82.125 12.433 1.00133.82 S ATOM 775 SG CYS A 101 52.641 79.333 10.773 1.00135.01 S ATOM 1162 SG CYS A 146 56.435 79.218 10.850 1.00135.96 S ATOM 1185 SG CYS A 149 54.749 81.813 8.683 1.00138.63 S ATOM 4568 SG CYS A 575 83.314 38.808 91.778 1.00101.43 S ATOM 4608 SG CYS A 580 81.407 37.971 92.061 1.00 95.71 S ATOM 15263 SG CYS B1060 26.489 62.648 33.979 1.00106.21 S ATOM 15286 SG CYS B1063 28.705 65.672 34.066 1.00104.50 S ATOM 15417 SG CYS B1078 24.964 66.062 34.528 1.00114.57 S ATOM 20467 SG CYS D 209 72.142 53.258 122.116 1.00 73.26 S ATOM 20421 SG CYS D 203 66.228 53.698 123.074 1.00 61.07 S ATOM 20443 SG CYS D 206 67.977 56.107 119.534 1.00 62.13 S ATOM 20268 SG CYS D 183 68.476 58.536 124.159 1.00 67.39 S ATOM 24411 SG CYS N 7 49.304 70.647 113.304 1.00 45.72 S ATOM 24435 SG CYS N 10 48.935 67.656 115.689 1.00 49.44 S ATOM 24698 SG CYS N 44 52.354 68.655 114.415 1.00 48.19 S ATOM 24704 SG CYS N 45 50.547 70.803 116.958 1.00 48.07 S ATOM 24932 SG CYS P 6 26.195 105.880 98.468 1.00 96.89 S ATOM 25082 SG CYS P 26 23.396 107.491 97.973 1.00103.51 S ATOM 25107 SG CYS P 29 26.386 108.729 98.722 1.00109.19 S Time building chain proxies: 14.12, per 1000 atoms: 0.55 Number of scatterers: 25636 At special positions: 0 Unit cell: (126.945, 149.73, 149.73, 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 6 29.99 Fe 3 26.01 S 122 16.00 Mg 1 11.99 O 4783 8.00 N 4427 7.00 C 16294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 29 " distance=2.04 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 119 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.43 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S D 301 " pdb="FE4 F3S D 301 " - pdb=" SG CYS D 183 " pdb="FE1 F3S D 301 " - pdb=" SG CYS D 209 " pdb="FE3 F3S D 301 " - pdb=" SG CYS D 203 " pdb="FE3 F3S D 301 " - pdb=" SG CYS D 206 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 71 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 61 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 68 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 58 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 98 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 101 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 149 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 580 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 575 " pdb="ZN ZN A 904 " - pdb=" ND1 HIS A 582 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" ND1 HIS B1081 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1063 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1060 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1078 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 29 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 6 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 26 " Number of angles added : 18 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6018 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 39 sheets defined 40.6% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 125 through 142 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.862A pdb=" N ARG A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.924A pdb=" N SER A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 228 " --> pdb=" O ILE A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 228' Processing helix chain 'A' and resid 233 through 256 removed outlier: 3.638A pdb=" N HIS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 278 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.753A pdb=" N LEU A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.843A pdb=" N TYR A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.941A pdb=" N ILE A 486 " --> pdb=" O HIS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.506A pdb=" N SER A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 610 through 642 removed outlier: 7.037A pdb=" N THR A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N GLU A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 654 through 680 removed outlier: 3.557A pdb=" N GLN A 658 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 718 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 776 through 779 removed outlier: 3.507A pdb=" N ARG A 779 " --> pdb=" O PRO A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 791 through 827 removed outlier: 4.985A pdb=" N GLU A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 878 through 880 No H-bonds generated for 'chain 'A' and resid 878 through 880' Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 21 through 34 Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.912A pdb=" N ILE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.901A pdb=" N ASN B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.536A pdb=" N SER B 241 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 removed outlier: 3.935A pdb=" N GLU B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.541A pdb=" N PHE B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 325 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 343 through 374 Processing helix chain 'B' and resid 378 through 384 removed outlier: 4.037A pdb=" N VAL B 383 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG B 384 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 removed outlier: 3.750A pdb=" N THR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 393 " --> pdb=" O THR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.737A pdb=" N GLY B 404 " --> pdb=" O TRP B 401 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 405 " --> pdb=" O VAL B 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 416 through 424 removed outlier: 3.513A pdb=" N MET B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.671A pdb=" N TRP B 448 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 4.156A pdb=" N VAL B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.661A pdb=" N SER B 514 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP B 515 " --> pdb=" O TYR B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 530 through 544 Processing helix chain 'B' and resid 588 through 596 Processing helix chain 'B' and resid 601 through 608 Processing helix chain 'B' and resid 617 through 622 Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.654A pdb=" N LEU B 631 " --> pdb=" O PRO B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 646 removed outlier: 3.931A pdb=" N ILE B 645 " --> pdb=" O PRO B 642 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 646 " --> pdb=" O SER B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 653 removed outlier: 3.694A pdb=" N ILE B 653 " --> pdb=" O ALA B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.710A pdb=" N ASN B 659 " --> pdb=" O PRO B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 672 removed outlier: 3.780A pdb=" N ASN B 664 " --> pdb=" O GLN B 660 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 709 removed outlier: 4.298A pdb=" N GLY B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 785 through 789 removed outlier: 4.367A pdb=" N LEU B 789 " --> pdb=" O TYR B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 911 No H-bonds generated for 'chain 'B' and resid 909 through 911' Processing helix chain 'B' and resid 912 through 917 removed outlier: 3.910A pdb=" N ARG B 916 " --> pdb=" O ALA B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 935 removed outlier: 4.239A pdb=" N ILE B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 959 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1028 through 1039 Processing helix chain 'B' and resid 1040 through 1049 Processing helix chain 'B' and resid 1094 through 1106 removed outlier: 3.691A pdb=" N MET B1106 " --> pdb=" O GLU B1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 67 through 78 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.729A pdb=" N MET C 83 " --> pdb=" O GLY C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 131 through 142 removed outlier: 3.604A pdb=" N ILE C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.614A pdb=" N GLY C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.773A pdb=" N ILE C 270 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.747A pdb=" N VAL C 278 " --> pdb=" O ASN C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 removed outlier: 3.543A pdb=" N ALA C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.819A pdb=" N ILE C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 removed outlier: 3.692A pdb=" N ARG C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 346 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 379 through 384 removed outlier: 3.716A pdb=" N VAL C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.836A pdb=" N ILE D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.941A pdb=" N TYR D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 262 Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 21 through 34 removed outlier: 4.184A pdb=" N ILE E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'H' and resid 24 through 36 Processing helix chain 'H' and resid 38 through 42 removed outlier: 3.667A pdb=" N LEU H 42 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 55 Processing helix chain 'K' and resid 4 through 15 Processing helix chain 'K' and resid 19 through 35 Processing helix chain 'K' and resid 51 through 63 Processing helix chain 'L' and resid 21 through 33 removed outlier: 3.890A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 88 Processing helix chain 'N' and resid 14 through 16 No H-bonds generated for 'chain 'N' and resid 14 through 16' Processing helix chain 'N' and resid 17 through 27 removed outlier: 3.587A pdb=" N PHE N 21 " --> pdb=" O LYS N 17 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN N 23 " --> pdb=" O GLU N 19 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET N 26 " --> pdb=" O SER N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 39 removed outlier: 3.537A pdb=" N VAL N 34 " --> pdb=" O ASP N 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY N 39 " --> pdb=" O LEU N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 51 Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'Q' and resid 39 through 58 Processing helix chain 'Q' and resid 62 through 79 removed outlier: 3.823A pdb=" N LYS Q 79 " --> pdb=" O ARG Q 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1111 through 1116 removed outlier: 6.270A pdb=" N ARG B1111 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 9 " --> pdb=" O ARG B1111 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B1113 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 82 removed outlier: 10.308A pdb=" N LEU A 77 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N LYS A 79 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 211 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.548A pdb=" N GLU A 151 " --> pdb=" O CYS A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.784A pdb=" N LYS A 157 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 165 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 316 through 318 Processing sheet with id=AA6, first strand: chain 'B' and resid 1001 through 1003 removed outlier: 3.650A pdb=" N HIS B1001 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.945A pdb=" N TYR A 377 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS A 410 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 375 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 516 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.736A pdb=" N CYS G 69 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G 10 " --> pdb=" O ASP G 28 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS G 26 " --> pdb=" O SER G 12 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE G 14 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL G 24 " --> pdb=" O ILE G 14 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ILE G 95 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU G 94 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE G 86 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU G 77 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU G 88 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 562 through 565 removed outlier: 3.588A pdb=" N GLU A 595 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LYS A 589 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 749 Processing sheet with id=AB3, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AB4, first strand: chain 'A' and resid 830 through 832 removed outlier: 6.813A pdb=" N VAL A 838 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 46 removed outlier: 5.637A pdb=" N SER B 97 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 60 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE B 95 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR B 62 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER B 92 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP B 116 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 94 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AB8, first strand: chain 'B' and resid 339 through 342 removed outlier: 6.468A pdb=" N ALA B 161 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 170 through 174 removed outlier: 3.847A pdb=" N HIS B 183 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC2, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AC3, first strand: chain 'B' and resid 523 through 528 removed outlier: 6.560A pdb=" N VAL B 518 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR B 527 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 516 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 566 " --> pdb=" O TYR B 519 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.683A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.683A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 848 " --> pdb=" O MET P 36 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET P 36 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 702 Processing sheet with id=AC7, first strand: chain 'B' and resid 718 through 719 removed outlier: 7.487A pdb=" N ILE B 736 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 889 " --> pdb=" O ILE B 736 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET B 738 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 723 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 983 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER B 980 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL B 969 " --> pdb=" O SER B 980 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 807 through 809 removed outlier: 6.876A pdb=" N ILE B 835 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 812 through 813 Processing sheet with id=AD1, first strand: chain 'B' and resid 1054 through 1060 Processing sheet with id=AD2, first strand: chain 'B' and resid 1068 through 1070 removed outlier: 3.611A pdb=" N ASP B1070 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG B1075 " --> pdb=" O ASP B1070 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 238 through 242 Processing sheet with id=AD4, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.767A pdb=" N SER C 153 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 203 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR C 205 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 198 " --> pdb=" O THR C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 57 through 59 removed outlier: 4.833A pdb=" N LEU C 386 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU C 385 " --> pdb=" O ARG K 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 3 through 8 removed outlier: 6.891A pdb=" N ARG D 14 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG D 8 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ILE D 219 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N VAL D 172 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N SER D 221 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N VAL D 170 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLU D 223 " --> pdb=" O PRO D 168 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS D 225 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TYR D 166 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 227 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 164 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU D 229 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER D 162 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLU D 231 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 115 through 116 removed outlier: 6.876A pdb=" N LYS D 138 " --> pdb=" O ASN D 49 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN D 49 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER D 140 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 43 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG D 146 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL D 41 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY D 148 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N MET D 39 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 107 through 110 removed outlier: 6.341A pdb=" N LEU D 107 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 132 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 109 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 188 through 189 Processing sheet with id=AE1, first strand: chain 'E' and resid 8 through 13 removed outlier: 3.522A pdb=" N GLU E 71 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS E 52 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.048A pdb=" N ILE H 45 " --> pdb=" O ILE H 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 2 through 8 removed outlier: 6.770A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU L 8 " --> pdb=" O TYR L 12 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 3027 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: 9.75 Time building geometry restraints manager: 10.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.83: 26064 1.83 - 2.43: 8 2.43 - 3.03: 0 3.03 - 3.64: 0 3.64 - 4.24: 3 Bond restraints: 26075 Sorted by residual: bond pdb=" S4 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.233 4.243 -2.010 2.00e-02 2.50e+03 1.01e+04 bond pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.258 4.230 -1.972 2.00e-02 2.50e+03 9.72e+03 bond pdb=" S2 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 2.300 4.187 -1.887 2.00e-02 2.50e+03 8.90e+03 bond pdb=" S2 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.317 2.202 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.296 2.192 0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 26070 not shown) Histogram of bond angle deviations from ideal: 39.39 - 61.54: 6 61.54 - 83.68: 6 83.68 - 105.82: 574 105.82 - 127.96: 34463 127.96 - 150.11: 158 Bond angle restraints: 35207 Sorted by residual: angle pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " pdb=" S3 F3S D 301 " ideal model delta sigma weight residual 114.75 39.54 75.21 3.00e+00 1.11e-01 6.29e+02 angle pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.59 39.39 73.20 3.00e+00 1.11e-01 5.95e+02 angle pdb=" S1 F3S D 301 " pdb="FE3 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.54 150.11 -37.57 3.00e+00 1.11e-01 1.57e+02 angle pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 74.86 43.55 31.31 3.00e+00 1.11e-01 1.09e+02 angle pdb="FE3 F3S D 301 " pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 73.06 43.65 29.41 3.00e+00 1.11e-01 9.61e+01 ... (remaining 35202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 14532 16.88 - 33.76: 1255 33.76 - 50.64: 223 50.64 - 67.52: 34 67.52 - 84.40: 17 Dihedral angle restraints: 16061 sinusoidal: 6697 harmonic: 9364 Sorted by residual: dihedral pdb=" CB CYS G 9 " pdb=" SG CYS G 9 " pdb=" SG CYS G 29 " pdb=" CB CYS G 29 " ideal model delta sinusoidal sigma weight residual 93.00 36.02 56.98 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS G 69 " pdb=" SG CYS G 69 " pdb=" SG CYS G 119 " pdb=" CB CYS G 119 " ideal model delta sinusoidal sigma weight residual 93.00 48.23 44.77 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA SER B1072 " pdb=" C SER B1072 " pdb=" N LYS B1073 " pdb=" CA LYS B1073 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 16058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.704: 3997 2.704 - 5.408: 0 5.408 - 8.111: 0 8.111 - 10.815: 0 10.815 - 13.519: 1 Chirality restraints: 3998 Sorted by residual: chirality pdb=" S2 F3S D 301 " pdb="FE1 F3S D 301 " pdb="FE3 F3S D 301 " pdb="FE4 F3S D 301 " both_signs ideal model delta sigma weight residual False 10.77 -2.75 13.52 2.00e-01 2.50e+01 4.57e+03 chirality pdb=" CA CYS G 69 " pdb=" N CYS G 69 " pdb=" C CYS G 69 " pdb=" CB CYS G 69 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 214 " pdb=" CA ILE C 214 " pdb=" CG1 ILE C 214 " pdb=" CG2 ILE C 214 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 3995 not shown) Planarity restraints: 4519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 39 " -0.036 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO P 40 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO P 40 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO P 40 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 39 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1069 " -0.013 2.00e-02 2.50e+03 1.21e-02 2.92e+00 pdb=" CG TYR B1069 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B1069 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B1069 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B1069 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B1069 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B1069 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1069 " 0.004 2.00e-02 2.50e+03 ... (remaining 4516 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 224 2.61 - 3.18: 21544 3.18 - 3.76: 37124 3.76 - 4.33: 54243 4.33 - 4.90: 92267 Nonbonded interactions: 205402 Sorted by model distance: nonbonded pdb=" OD1 ASP A 456 " pdb="MG MG A 901 " model vdw 2.038 2.170 nonbonded pdb=" OD2 ASP A 460 " pdb="MG MG A 901 " model vdw 2.056 2.170 nonbonded pdb=" OD1 ASP A 460 " pdb="MG MG A 901 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR D 171 " pdb=" OG SER D 218 " model vdw 2.067 3.040 nonbonded pdb=" OD2 ASP A 458 " pdb="MG MG A 901 " model vdw 2.076 2.170 ... (remaining 205397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.230 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: 0.000 Extract box with map and model: 0.790 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 75.330 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.021 2.010 26075 Z= 1.207 Angle : 0.929 75.214 35207 Z= 0.379 Chirality : 0.218 13.519 3998 Planarity : 0.004 0.056 4519 Dihedral : 12.908 84.403 10037 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.12 (0.15), residues: 3202 helix: 1.05 (0.16), residues: 1140 sheet: 0.30 (0.24), residues: 481 loop : -0.68 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.024 0.001 PHE A 419 TYR 0.029 0.001 TYR B1069 ARG 0.006 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.793 Fit side-chains REVERT: A 1 MET cc_start: 0.6106 (tmm) cc_final: 0.5661 (tmm) REVERT: A 159 GLU cc_start: 0.7795 (tp30) cc_final: 0.7586 (tp30) REVERT: B 390 GLU cc_start: 0.7894 (tp30) cc_final: 0.7683 (tp30) REVERT: C 133 ASP cc_start: 0.7233 (p0) cc_final: 0.7032 (t0) REVERT: C 252 ASP cc_start: 0.7462 (t0) cc_final: 0.7160 (t0) REVERT: C 301 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7491 (tm-30) REVERT: D 118 ASP cc_start: 0.8328 (t70) cc_final: 0.7965 (t0) REVERT: E 69 GLU cc_start: 0.7256 (tt0) cc_final: 0.7005 (tt0) REVERT: H 21 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7518 (mt-10) REVERT: L 1 MET cc_start: 0.7444 (ttt) cc_final: 0.7128 (ttt) REVERT: P 16 ASP cc_start: 0.8271 (p0) cc_final: 0.7920 (p0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 1.7225 time to fit residues: 724.4799 Evaluate side-chains 281 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 0.0970 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS A 420 ASN A 739 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 HIS B1009 GLN C 199 ASN C 326 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 26075 Z= 0.238 Angle : 0.888 77.673 35207 Z= 0.368 Chirality : 0.065 2.948 3998 Planarity : 0.004 0.049 4519 Dihedral : 4.008 20.641 3559 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.31 % Allowed : 8.17 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.19 (0.15), residues: 3202 helix: 1.13 (0.16), residues: 1170 sheet: 0.27 (0.23), residues: 497 loop : -0.67 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.020 0.001 PHE A 419 TYR 0.018 0.001 TYR G 118 ARG 0.009 0.000 ARG P 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 307 time to evaluate : 2.984 Fit side-chains revert: symmetry clash REVERT: A 230 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.6872 (ptp-110) REVERT: A 822 ARG cc_start: 0.7371 (mtp85) cc_final: 0.7135 (mtm110) REVERT: B 390 GLU cc_start: 0.7493 (tp30) cc_final: 0.7281 (tm-30) REVERT: B 768 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: C 133 ASP cc_start: 0.7212 (p0) cc_final: 0.6988 (t0) REVERT: C 215 MET cc_start: 0.7011 (tpp) cc_final: 0.6579 (tpt) REVERT: C 252 ASP cc_start: 0.7465 (t0) cc_final: 0.7147 (t0) REVERT: D 118 ASP cc_start: 0.8401 (t70) cc_final: 0.7979 (t0) REVERT: G 106 ASN cc_start: 0.8861 (t0) cc_final: 0.8433 (t0) REVERT: H 21 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7473 (mt-10) REVERT: K 46 ASN cc_start: 0.8266 (t0) cc_final: 0.7522 (t0) REVERT: P 16 ASP cc_start: 0.8095 (p0) cc_final: 0.7752 (p0) REVERT: Q 48 LYS cc_start: 0.8251 (mttt) cc_final: 0.7967 (mttp) REVERT: Q 58 ARG cc_start: 0.8626 (mtp180) cc_final: 0.8310 (mtp180) outliers start: 37 outliers final: 17 residues processed: 326 average time/residue: 1.6658 time to fit residues: 617.8943 Evaluate side-chains 297 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain P residue 46 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 0.0870 chunk 232 optimal weight: 0.7980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS B 793 ASN B 921 GLN B1001 HIS ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 26075 Z= 0.258 Angle : 0.732 79.044 35207 Z= 0.326 Chirality : 0.052 1.677 3998 Planarity : 0.004 0.052 4519 Dihedral : 4.054 20.721 3559 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.46 % Allowed : 10.66 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.16 (0.15), residues: 3202 helix: 1.18 (0.16), residues: 1167 sheet: 0.25 (0.23), residues: 506 loop : -0.75 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.016 0.001 PHE A 419 TYR 0.021 0.001 TYR G 118 ARG 0.012 0.000 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 292 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7982 (mtpp) REVERT: B 390 GLU cc_start: 0.7531 (tp30) cc_final: 0.7261 (tm-30) REVERT: B 738 MET cc_start: 0.8922 (mtp) cc_final: 0.8695 (ttm) REVERT: B 768 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: C 252 ASP cc_start: 0.7471 (t0) cc_final: 0.7146 (t0) REVERT: C 329 ARG cc_start: 0.6902 (tpt170) cc_final: 0.6460 (tpt170) REVERT: C 360 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: D 7 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: D 118 ASP cc_start: 0.8406 (t70) cc_final: 0.7975 (t0) REVERT: E 71 GLU cc_start: 0.7777 (mt-10) cc_final: 0.6878 (mp0) REVERT: H 21 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7463 (mt-10) REVERT: L 39 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8862 (mmmm) REVERT: P 16 ASP cc_start: 0.8012 (p0) cc_final: 0.7674 (p0) REVERT: Q 48 LYS cc_start: 0.8234 (mttt) cc_final: 0.7991 (mttp) outliers start: 41 outliers final: 16 residues processed: 312 average time/residue: 1.6006 time to fit residues: 566.7657 Evaluate side-chains 289 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 269 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain P residue 46 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.6980 chunk 217 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 138 optimal weight: 0.0050 chunk 194 optimal weight: 9.9990 chunk 290 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 275 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 26075 Z= 0.199 Angle : 0.718 81.741 35207 Z= 0.317 Chirality : 0.050 1.536 3998 Planarity : 0.004 0.054 4519 Dihedral : 3.978 21.578 3559 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.56 % Allowed : 11.83 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.24 (0.15), residues: 3202 helix: 1.26 (0.16), residues: 1163 sheet: 0.29 (0.23), residues: 498 loop : -0.71 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.012 0.001 PHE A 419 TYR 0.020 0.001 TYR B1069 ARG 0.009 0.000 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 283 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.7775 (tp30) cc_final: 0.7488 (pt0) REVERT: A 788 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7736 (ttp80) REVERT: B 390 GLU cc_start: 0.7515 (tp30) cc_final: 0.7241 (tm-30) REVERT: B 768 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: C 215 MET cc_start: 0.7266 (tpp) cc_final: 0.6917 (tpt) REVERT: C 252 ASP cc_start: 0.7446 (t0) cc_final: 0.7136 (t0) REVERT: C 329 ARG cc_start: 0.7096 (tpt170) cc_final: 0.6597 (tpt170) REVERT: C 360 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: D 118 ASP cc_start: 0.8384 (t70) cc_final: 0.7939 (t0) REVERT: E 71 GLU cc_start: 0.7778 (mt-10) cc_final: 0.6906 (mp0) REVERT: H 21 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7450 (mt-10) REVERT: K 46 ASN cc_start: 0.8289 (t0) cc_final: 0.7722 (t0) REVERT: L 39 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8841 (mmmm) REVERT: P 16 ASP cc_start: 0.7935 (p0) cc_final: 0.7607 (p0) REVERT: Q 48 LYS cc_start: 0.8279 (mttt) cc_final: 0.8057 (mttp) REVERT: Q 71 ASP cc_start: 0.7848 (p0) cc_final: 0.7636 (p0) outliers start: 44 outliers final: 17 residues processed: 307 average time/residue: 1.6139 time to fit residues: 565.5657 Evaluate side-chains 295 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 275 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 788 ARG Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain P residue 46 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 126 optimal weight: 0.3980 chunk 262 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: