Starting phenix.real_space_refine on Sun Mar 24 23:36:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gml_0038/03_2024/6gml_0038_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gml_0038/03_2024/6gml_0038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gml_0038/03_2024/6gml_0038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gml_0038/03_2024/6gml_0038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gml_0038/03_2024/6gml_0038_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gml_0038/03_2024/6gml_0038_neut.pdb" } resolution = 3.2 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= 0.002 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 9 6.06 5 P 98 5.49 5 Mg 1 5.21 5 S 246 5.16 5 C 27762 2.51 5 N 7991 2.21 5 O 8720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A ARG 1167": "NH1" <-> "NH2" Residue "A TYR 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1213": "NH1" <-> "NH2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ARG 1408": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B ARG 886": "NH1" <-> "NH2" Residue "B TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 42": "NH1" <-> "NH2" Residue "U PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 206": "NH1" <-> "NH2" Residue "W ARG 347": "NH1" <-> "NH2" Residue "W ARG 439": "NH1" <-> "NH2" Residue "Z ARG 198": "NH1" <-> "NH2" Residue "Z ARG 555": "NH1" <-> "NH2" Residue "Z ARG 571": "NH1" <-> "NH2" Residue "Z ARG 577": "NH1" <-> "NH2" Residue "Z ARG 582": "NH1" <-> "NH2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44827 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11142 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8928 Classifications: {'peptide': 1116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1062} Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 730 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "P" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "T" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 933 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "U" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1410 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "V" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 1932 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 463} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain breaks: 7 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1993 Unresolved non-hydrogen angles: 2888 Unresolved non-hydrogen dihedrals: 1241 Unresolved non-hydrogen chiralities: 606 Planarities with less than four sites: {'GLN:plan1': 21, 'ASN:plan1': 8, 'ASP:plan': 24, 'TYR:plan': 9, 'UNK:plan-1': 38, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 26, 'GLU:plan': 36, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 881 Chain: "W" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 3858 Classifications: {'peptide': 538} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 516} Chain breaks: 2 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 3, 'TYR:plan': 2, 'UNK:plan-1': 41, 'TRP:plan': 3, 'HIS:plan': 4, 'ARG:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 224 Chain: "X" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3770 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 16, 'TRANS': 453} Chain breaks: 7 Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" 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 768 SG CYS A 111 93.380 72.431 137.194 1.00 52.15 S ATOM 796 SG CYS A 114 93.723 72.406 141.521 1.00 60.58 S ATOM 464 SG CYS A 71 47.340 71.891 125.479 1.00 41.25 S ATOM 486 SG CYS A 74 47.060 75.962 124.614 1.00 35.32 S ATOM 533 SG CYS A 81 48.143 73.806 121.757 1.00 35.83 S ATOM 19639 SG CYS B1119 58.135 85.562 129.404 1.00 32.24 S ATOM 19661 SG CYS B1122 61.242 83.877 130.290 1.00 35.98 S ATOM 19776 SG CYS B1137 57.759 82.371 130.958 1.00 48.78 S ATOM 20764 SG CYS C 88 11.221 76.621 66.450 1.00 27.25 S ATOM 20777 SG CYS C 90 11.932 73.821 69.028 1.00 37.75 S ATOM 20812 SG CYS C 94 11.056 73.106 65.533 1.00 23.11 S ATOM 20834 SG CYS C 97 14.614 73.590 65.899 1.00 16.65 S ATOM 25776 SG CYS I 17 125.353 34.343 92.308 1.00 39.89 S ATOM 25800 SG CYS I 20 122.701 34.499 94.757 1.00 41.99 S ATOM 25961 SG CYS I 39 124.020 37.747 95.721 1.00 38.99 S ATOM 25986 SG CYS I 42 126.257 34.422 95.826 1.00 43.23 S ATOM 26338 SG CYS I 86 113.852 47.359 51.643 1.00 32.07 S ATOM 26362 SG CYS I 89 112.826 44.359 49.722 1.00 31.64 S ATOM 26601 SG CYS I 119 111.302 43.030 52.749 1.00 38.63 S ATOM 26712 SG CYS J 7 42.310 68.307 52.595 1.00 28.01 S ATOM 26736 SG CYS J 10 41.342 72.018 49.781 1.00 23.57 S ATOM 27000 SG CYS J 44 44.557 70.683 50.305 1.00 23.69 S ATOM 27006 SG CYS J 45 41.593 68.124 48.967 1.00 21.59 S ATOM 28187 SG CYS L 22 33.873 32.997 80.209 1.00 35.66 S ATOM 28304 SG CYS L 36 31.961 33.302 83.247 1.00 37.97 S ATOM 37952 SG CYS Y 16 70.632 21.433 150.340 1.00 81.24 S ATOM 37974 SG CYS Y 19 74.637 21.329 148.716 1.00 84.47 S ATOM 38086 SG CYS Y 33 73.062 17.922 148.915 1.00 73.71 S Time building chain proxies: 24.09, per 1000 atoms: 0.54 Number of scatterers: 44827 At special positions: 0 Unit cell: (155.918, 186.61, 185.383, 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 9 29.99 S 246 16.00 P 98 15.00 Mg 1 11.99 O 8720 8.00 N 7991 7.00 C 27762 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 - 3.50 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: 17.43 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 21 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9804 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 58 sheets defined 43.5% alpha, 15.2% beta 44 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 14.38 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.601A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.695A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.499A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.326A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.714A pdb=" N ASP A 437 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 438' Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 662 through 684 removed outlier: 4.070A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.844A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 removed outlier: 3.625A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 757 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.638A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.556A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.105A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.531A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.891A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 4.156A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.835A pdb=" N TRP A1192 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A1194 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.785A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.533A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1294 removed outlier: 3.994A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.853A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.750A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.648A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.323A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.270A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.742A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.687A pdb=" N VAL B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.934A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 450 removed outlier: 4.196A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.656A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.605A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.646A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.502A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.513A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 968 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.968A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.862A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.645A pdb=" N ARG B1080 " --> pdb=" O GLY B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.709A pdb=" N ASN C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.925A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.565A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.422A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.615A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.811A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.525A pdb=" N GLY F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.948A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.201A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.826A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.549A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.965A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.780A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 5.811A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 3.726A pdb=" N THR K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 18 Processing helix chain 'U' and resid 34 through 42 Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 64 through 71 removed outlier: 3.789A pdb=" N MET U 71 " --> pdb=" O THR U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 84 removed outlier: 3.558A pdb=" N LEU U 75 " --> pdb=" O MET U 71 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU U 84 " --> pdb=" O GLN U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 98 Processing helix chain 'U' and resid 114 through 131 removed outlier: 3.550A pdb=" N GLN U 118 " --> pdb=" O ASN U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 143 removed outlier: 3.836A pdb=" N GLN U 142 " --> pdb=" O LEU U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 154 removed outlier: 3.543A pdb=" N GLY U 154 " --> pdb=" O THR U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 187 removed outlier: 4.080A pdb=" N THR U 173 " --> pdb=" O PRO U 169 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.614A pdb=" N UNK V 12 " --> pdb=" O UNK V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 35 removed outlier: 4.032A pdb=" N UNK V 35 " --> pdb=" O UNK V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 52 Proline residue: V 49 - end of helix Processing helix chain 'V' and resid 57 through 80 removed outlier: 3.683A pdb=" N PHE V 61 " --> pdb=" O PRO V 57 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS V 72 " --> pdb=" O GLU V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 103 Processing helix chain 'V' and resid 110 through 119 removed outlier: 4.168A pdb=" N HIS V 119 " --> pdb=" O CYS V 115 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 133 removed outlier: 3.528A pdb=" N ALA V 133 " --> pdb=" O LYS V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 138 through 143 Processing helix chain 'V' and resid 155 through 176 removed outlier: 4.162A pdb=" N SER V 162 " --> pdb=" O GLY V 158 " (cutoff:3.500A) Proline residue: V 163 - end of helix Processing helix chain 'V' and resid 200 through 207 Processing helix chain 'V' and resid 211 through 230 Processing helix chain 'V' and resid 233 through 243 removed outlier: 3.632A pdb=" N LEU V 237 " --> pdb=" O HIS V 233 " (cutoff:3.500A) Processing helix chain 'V' and resid 260 through 273 removed outlier: 4.630A pdb=" N CYS V 269 " --> pdb=" O CYS V 265 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE V 270 " --> pdb=" O LEU V 266 " (cutoff:3.500A) Processing helix chain 'V' and resid 277 through 289 removed outlier: 3.648A pdb=" N GLY V 289 " --> pdb=" O GLY V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 295 through 306 removed outlier: 3.648A pdb=" N CYS V 306 " --> pdb=" O SER V 302 " (cutoff:3.500A) Processing helix chain 'V' and resid 307 through 329 Processing helix chain 'V' and resid 339 through 352 Processing helix chain 'V' and resid 367 through 387 removed outlier: 3.910A pdb=" N THR V 371 " --> pdb=" O VAL V 367 " (cutoff:3.500A) Proline residue: V 375 - end of helix Processing helix chain 'V' and resid 409 through 417 Processing helix chain 'V' and resid 421 through 429 Processing helix chain 'V' and resid 439 through 453 Proline residue: V 446 - end of helix Processing helix chain 'V' and resid 459 through 475 Processing helix chain 'V' and resid 476 through 489 Processing helix chain 'V' and resid 495 through 508 Processing helix chain 'V' and resid 515 through 525 removed outlier: 3.788A pdb=" N GLN V 524 " --> pdb=" O LEU V 520 " (cutoff:3.500A) Processing helix chain 'V' and resid 532 through 547 removed outlier: 3.542A pdb=" N ALA V 536 " --> pdb=" O GLN V 532 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 60 removed outlier: 3.951A pdb=" N UNK W 60 " --> pdb=" O UNK W 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 57 through 60' Processing helix chain 'W' and resid 61 through 71 removed outlier: 3.576A pdb=" N UNK W 65 " --> pdb=" O UNK W 61 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N UNK W 71 " --> pdb=" O UNK W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 84 Processing helix chain 'W' and resid 90 through 105 removed outlier: 4.036A pdb=" N LEU W 96 " --> pdb=" O GLN W 92 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU W 99 " --> pdb=" O ASN W 95 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP W 100 " --> pdb=" O LEU W 96 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR W 104 " --> pdb=" O TRP W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 127 Processing helix chain 'W' and resid 132 through 140 removed outlier: 3.980A pdb=" N GLY W 140 " --> pdb=" O PHE W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 152 removed outlier: 3.548A pdb=" N GLU W 147 " --> pdb=" O PRO W 143 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 164 removed outlier: 3.798A pdb=" N GLU W 164 " --> pdb=" O TYR W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 182 Processing helix chain 'W' and resid 197 through 216 removed outlier: 3.790A pdb=" N ARG W 203 " --> pdb=" O GLU W 199 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 223 removed outlier: 4.063A pdb=" N LYS W 222 " --> pdb=" O GLU W 218 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 232 removed outlier: 4.942A pdb=" N MET W 230 " --> pdb=" O GLU W 226 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL W 231 " --> pdb=" O PHE W 227 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 249 Processing helix chain 'W' and resid 254 through 273 removed outlier: 4.357A pdb=" N VAL W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 284 Processing helix chain 'W' and resid 285 through 288 Processing helix chain 'W' and resid 289 through 303 removed outlier: 3.600A pdb=" N CYS W 293 " --> pdb=" O TYR W 289 " (cutoff:3.500A) Processing helix chain 'W' and resid 306 through 317 removed outlier: 3.617A pdb=" N MET W 316 " --> pdb=" O VAL W 312 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 328 Processing helix chain 'W' and resid 330 through 343 removed outlier: 3.805A pdb=" N LYS W 343 " --> pdb=" O GLN W 339 " (cutoff:3.500A) Processing helix chain 'W' and resid 352 through 366 removed outlier: 3.980A pdb=" N VAL W 366 " --> pdb=" O TYR W 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 382 through 400 removed outlier: 4.177A pdb=" N GLU W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 401 through 410 Processing helix chain 'W' and resid 410 through 418 Processing helix chain 'W' and resid 420 through 436 Processing helix chain 'W' and resid 449 through 462 Processing helix chain 'W' and resid 465 through 479 Processing helix chain 'W' and resid 485 through 506 Processing helix chain 'W' and resid 509 through 522 Processing helix chain 'W' and resid 526 through 539 removed outlier: 3.642A pdb=" N ILE W 530 " --> pdb=" O ASP W 526 " (cutoff:3.500A) Processing helix chain 'W' and resid 546 through 559 Proline residue: W 555 - end of helix Processing helix chain 'W' and resid 562 through 566 removed outlier: 3.601A pdb=" N THR W 565 " --> pdb=" O ILE W 562 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE W 566 " --> pdb=" O ALA W 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 562 through 566' Processing helix chain 'W' and resid 575 through 586 Processing helix chain 'X' and resid 4 through 18 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 removed outlier: 3.643A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 3.653A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 245 through 249 removed outlier: 3.563A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.718A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 removed outlier: 3.547A pdb=" N GLY Z 349 " --> pdb=" O ILE Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 630 through 633 removed outlier: 4.186A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.516A pdb=" N GLN D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 16 through 20' Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.627A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.931A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.554A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 362 through 369 removed outlier: 8.134A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.723A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.550A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.224A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL B 794 " --> pdb=" O CYS B 945 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 947 " --> pdb=" O VAL B 794 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.224A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.954A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1139 through 1140 removed outlier: 3.706A pdb=" N THR A1140 " --> pdb=" O THR A1358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 3.999A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1308 through 1310 Processing sheet with id=AB9, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC1, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.736A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.541A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.349A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.795A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC8, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC9, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.177A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.683A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.683A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 removed outlier: 7.344A pdb=" N GLN B 838 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.526A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD7, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.827A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.333A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AE2, first strand: chain 'E' and resid 102 through 105 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE4, first strand: chain 'H' and resid 139 through 142 removed outlier: 3.847A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AE6, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE7, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE8, first strand: chain 'U' and resid 164 through 165 Processing sheet with id=AE9, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF1, first strand: chain 'Y' and resid 83 through 90 removed outlier: 7.117A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 278 through 280 removed outlier: 6.756A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 352 through 355 Processing sheet with id=AF4, first strand: chain 'Z' and resid 453 through 454 Processing sheet with id=AF5, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.270A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.493A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AF8, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.656A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.953A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.754A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.754A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.525A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 118 through 120 1990 hydrogen bonds defined for protein. 5631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 24.14 Time building geometry restraints manager: 18.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9130 1.33 - 1.45: 10582 1.45 - 1.57: 25514 1.57 - 1.69: 192 1.69 - 1.81: 388 Bond restraints: 45806 Sorted by residual: bond pdb=" CA PRO U 26 " pdb=" C PRO U 26 " ideal model delta sigma weight residual 1.517 1.493 0.024 6.70e-03 2.23e+04 1.30e+01 bond pdb=" N LEU W 523 " pdb=" CA LEU W 523 " ideal model delta sigma weight residual 1.462 1.507 -0.046 1.31e-02 5.83e+03 1.22e+01 bond pdb=" CG LEU B 505 " pdb=" CD2 LEU B 505 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.77e+00 bond pdb=" C PHE B 713 " pdb=" O PHE B 713 " ideal model delta sigma weight residual 1.233 1.220 0.013 4.80e-03 4.34e+04 6.96e+00 bond pdb=" N LYS A1115 " pdb=" CA LYS A1115 " ideal model delta sigma weight residual 1.462 1.499 -0.037 1.48e-02 4.57e+03 6.42e+00 ... (remaining 45801 not shown) Histogram of bond angle deviations from ideal: 95.37 - 103.38: 756 103.38 - 111.40: 18634 111.40 - 119.41: 19457 119.41 - 127.42: 22757 127.42 - 135.44: 552 Bond angle restraints: 62156 Sorted by residual: angle pdb=" C ILE W 418 " pdb=" CA ILE W 418 " pdb=" CB ILE W 418 " ideal model delta sigma weight residual 111.29 120.82 -9.53 1.64e+00 3.72e-01 3.38e+01 angle pdb=" N ILE W 418 " pdb=" CA ILE W 418 " pdb=" CB ILE W 418 " ideal model delta sigma weight residual 111.23 102.27 8.96 1.65e+00 3.67e-01 2.95e+01 angle pdb=" C PRO K 79 " pdb=" N ASP K 80 " pdb=" CA ASP K 80 " ideal model delta sigma weight residual 125.66 135.44 -9.78 1.85e+00 2.92e-01 2.79e+01 angle pdb=" C GLU C 91 " pdb=" N GLU C 92 " pdb=" CA GLU C 92 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" N LEU V 305 " pdb=" CA LEU V 305 " pdb=" C LEU V 305 " ideal model delta sigma weight residual 110.97 116.42 -5.45 1.09e+00 8.42e-01 2.50e+01 ... (remaining 62151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 26290 32.78 - 65.55: 760 65.55 - 98.33: 52 98.33 - 131.10: 1 131.10 - 163.88: 2 Dihedral angle restraints: 27105 sinusoidal: 11515 harmonic: 15590 Sorted by residual: dihedral pdb=" CA HIS A1108 " pdb=" C HIS A1108 " pdb=" N TYR A1109 " pdb=" CA TYR A1109 " ideal model delta harmonic sigma weight residual 180.00 129.46 50.54 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA GLU B 629 " pdb=" C GLU B 629 " pdb=" N LYS B 630 " pdb=" CA LYS B 630 " ideal model delta harmonic sigma weight residual -180.00 -133.36 -46.64 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 141.45 38.55 0 5.00e+00 4.00e-02 5.95e+01 ... (remaining 27102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5864 0.083 - 0.167: 855 0.167 - 0.250: 51 0.250 - 0.333: 8 0.333 - 0.417: 6 Chirality restraints: 6784 Sorted by residual: chirality pdb=" CG LEU A 405 " pdb=" CB LEU A 405 " pdb=" CD1 LEU A 405 " pdb=" CD2 LEU A 405 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CB ILE B 621 " pdb=" CA ILE B 621 " pdb=" CG1 ILE B 621 " pdb=" CG2 ILE B 621 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 6781 not shown) Planarity restraints: 7864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN W 401 " 0.025 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C ASN W 401 " -0.085 2.00e-02 2.50e+03 pdb=" O ASN W 401 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA W 404 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER U 182 " 0.025 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C SER U 182 " -0.083 2.00e-02 2.50e+03 pdb=" O SER U 182 " 0.031 2.00e-02 2.50e+03 pdb=" N THR U 183 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN W 444 " -0.024 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C GLN W 444 " 0.081 2.00e-02 2.50e+03 pdb=" O GLN W 444 " -0.030 2.00e-02 2.50e+03 pdb=" N THR W 445 " -0.027 2.00e-02 2.50e+03 ... (remaining 7861 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 455 2.62 - 3.19: 37857 3.19 - 3.76: 70432 3.76 - 4.33: 96533 4.33 - 4.90: 156715 Nonbonded interactions: 361992 Sorted by model distance: nonbonded pdb=" NE2 GLN W 444 " pdb=" OE2 GLU W 488 " model vdw 2.054 2.520 nonbonded pdb=" OD2 ASP Y 58 " pdb=" NZ LYS Z 268 " model vdw 2.057 2.520 nonbonded pdb=" OD2 ASP B 851 " pdb=" OH TYR L 17 " model vdw 2.084 2.440 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.095 2.170 nonbonded pdb=" NZ LYS A 149 " pdb=" OP2 DG T 14 " model vdw 2.108 2.520 ... (remaining 361987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.680 Check model and map are aligned: 0.760 Set scattering table: 0.510 Process input model: 135.640 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 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 : 0.007 0.137 45806 Z= 0.487 Angle : 0.971 13.632 62156 Z= 0.522 Chirality : 0.059 0.417 6784 Planarity : 0.007 0.104 7864 Dihedral : 13.653 163.877 17301 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 0.43 % Allowed : 4.74 % Favored : 94.83 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.09), residues: 5485 helix: -2.34 (0.08), residues: 2176 sheet: -2.09 (0.18), residues: 664 loop : -2.33 (0.11), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP B 573 HIS 0.017 0.003 HIS A 721 PHE 0.051 0.004 PHE A 482 TYR 0.049 0.003 TYR B1048 ARG 0.014 0.001 ARG B 924 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 956 time to evaluate : 5.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 968 ASN cc_start: 0.6432 (t0) cc_final: 0.5821 (t0) REVERT: E 49 SER cc_start: 0.6578 (m) cc_final: 0.6074 (p) REVERT: Z 222 LYS cc_start: 0.4238 (mttp) cc_final: 0.3763 (pttp) outliers start: 19 outliers final: 4 residues processed: 969 average time/residue: 0.6007 time to fit residues: 927.7142 Evaluate side-chains 431 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 427 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain W residue 330 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 477 optimal weight: 50.0000 chunk 429 optimal weight: 50.0000 chunk 238 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 289 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 443 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 330 optimal weight: 0.8980 chunk 513 optimal weight: 30.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN A 272 ASN A 293 ASN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 432 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 507 GLN A 576 GLN A 609 HIS A 654 HIS A 662 HIS ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 809 HIS A 861 GLN A 905 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1093 GLN A1101 GLN A1129 ASN A1163 HIS A1244 ASN A1248 ASN A1299 GLN A1332 GLN A1457 ASN B 111 ASN B 486 ASN B 518 HIS B 577 HIS B 639 HIS B 650 ASN B 699 HIS B 749 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS B1003 ASN B1021 HIS B1040 GLN B1094 GLN B1133 HIS C 55 ASN C 232 ASN E 107 GLN E 132 GLN E 148 HIS E 168 ASN H 76 ASN I 22 ASN I 41 ASN I 91 HIS I 100 HIS K 2 ASN K 49 GLN U 80 GLN U 142 GLN U 145 ASN U 147 ASN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 352 HIS W 394 HIS W 451 HIS W 502 HIS Y 12 HIS Y 41 GLN Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 45806 Z= 0.213 Angle : 0.630 10.323 62156 Z= 0.328 Chirality : 0.044 0.283 6784 Planarity : 0.005 0.077 7864 Dihedral : 14.649 166.020 7245 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 2.37 % Allowed : 10.86 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.10), residues: 5485 helix: -0.31 (0.10), residues: 2200 sheet: -1.73 (0.18), residues: 681 loop : -1.80 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 988 HIS 0.011 0.001 HIS Z 220 PHE 0.033 0.002 PHE A 458 TYR 0.022 0.002 TYR W 415 ARG 0.009 0.001 ARG W 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 468 time to evaluate : 5.488 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: A 238 MET cc_start: 0.6150 (ttm) cc_final: 0.5937 (ttm) REVERT: A 1127 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7502 (mt) REVERT: B 968 ASN cc_start: 0.6116 (t0) cc_final: 0.5697 (t0) REVERT: W 566 ILE cc_start: 0.5261 (OUTLIER) cc_final: 0.5053 (tp) REVERT: Y 42 MET cc_start: 0.0593 (mpp) cc_final: 0.0321 (tmm) REVERT: Z 222 LYS cc_start: 0.4119 (mttp) cc_final: 0.3740 (pttp) REVERT: Z 359 LEU cc_start: 0.1489 (OUTLIER) cc_final: 0.1145 (mp) REVERT: Z 373 PHE cc_start: 0.2299 (OUTLIER) cc_final: 0.1994 (t80) REVERT: D 34 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6906 (m110) outliers start: 105 outliers final: 41 residues processed: 544 average time/residue: 0.5427 time to fit residues: 497.6539 Evaluate side-chains 414 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 368 time to evaluate : 5.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 469 VAL Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 566 ILE Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 373 PHE Chi-restraints excluded: chain D residue 34 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 285 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 427 optimal weight: 50.0000 chunk 349 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 514 optimal weight: 20.0000 chunk 556 optimal weight: 7.9990 chunk 458 optimal weight: 0.9980 chunk 510 optimal weight: 50.0000 chunk 175 optimal weight: 5.9990 chunk 413 optimal weight: 30.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN A 313 HIS A 330 GLN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 439 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN A 780 ASN A 989 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 HIS A1310 HIS B 111 ASN B 481 HIS B 649 ASN B 941 GLN B1009 GLN ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS E 43 GLN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN J 52 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN U 147 ASN W 253 GLN W 270 GLN W 354 HIS Z 220 HIS Z 232 GLN Z 616 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN G 9 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 45806 Z= 0.409 Angle : 0.705 11.394 62156 Z= 0.367 Chirality : 0.046 0.217 6784 Planarity : 0.005 0.099 7864 Dihedral : 14.459 165.021 7245 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.52 % Favored : 94.44 % Rotamer: Outliers : 3.30 % Allowed : 11.72 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.11), residues: 5485 helix: 0.50 (0.11), residues: 2225 sheet: -1.43 (0.18), residues: 685 loop : -1.47 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 548 HIS 0.043 0.002 HIS I 100 PHE 0.028 0.002 PHE A 668 TYR 0.040 0.002 TYR B1048 ARG 0.008 0.001 ARG Z 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 375 time to evaluate : 5.271 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: A 535 MET cc_start: 0.8079 (mmt) cc_final: 0.7848 (mmm) REVERT: A 1428 MET cc_start: 0.7315 (tpp) cc_final: 0.6702 (ttt) REVERT: B 508 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7114 (mpp) REVERT: B 674 MET cc_start: 0.7963 (tpt) cc_final: 0.7741 (tpt) REVERT: B 1151 MET cc_start: 0.7748 (ptp) cc_final: 0.7474 (ptm) REVERT: I 60 HIS cc_start: 0.5233 (t-90) cc_final: 0.2942 (t70) REVERT: Z 373 PHE cc_start: 0.1486 (OUTLIER) cc_final: 0.1188 (t80) REVERT: G 117 MET cc_start: 0.2258 (mmm) cc_final: 0.2008 (tpp) outliers start: 146 outliers final: 68 residues processed: 493 average time/residue: 0.5347 time to fit residues: 443.8649 Evaluate side-chains 396 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 326 time to evaluate : 5.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 125 TYR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 413 THR Chi-restraints excluded: chain W residue 469 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 373 PHE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 730 SER Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 508 optimal weight: 0.8980 chunk 387 optimal weight: 50.0000 chunk 267 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 245 optimal weight: 0.0670 chunk 345 optimal weight: 0.9980 chunk 516 optimal weight: 40.0000 chunk 547 optimal weight: 0.2980 chunk 269 optimal weight: 0.3980 chunk 489 optimal weight: 0.0770 chunk 147 optimal weight: 30.0000 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 387 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 HIS Z 593 ASN ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 45806 Z= 0.149 Angle : 0.563 8.106 62156 Z= 0.290 Chirality : 0.042 0.191 6784 Planarity : 0.004 0.055 7864 Dihedral : 14.309 168.653 7243 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.96 % Allowed : 13.05 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.52 (0.11), residues: 5485 helix: 1.03 (0.11), residues: 2223 sheet: -1.24 (0.18), residues: 714 loop : -1.31 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 548 HIS 0.018 0.001 HIS A 313 PHE 0.023 0.001 PHE A 312 TYR 0.021 0.001 TYR W 415 ARG 0.009 0.000 ARG Z 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 364 time to evaluate : 5.224 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: A 1428 MET cc_start: 0.7200 (tpp) cc_final: 0.6609 (ttt) REVERT: H 42 ASP cc_start: 0.7158 (m-30) cc_final: 0.6958 (m-30) REVERT: W 566 ILE cc_start: 0.5702 (OUTLIER) cc_final: 0.5418 (tp) REVERT: Y 42 MET cc_start: 0.1139 (mpp) cc_final: 0.0572 (tmm) REVERT: Z 245 LEU cc_start: 0.3375 (OUTLIER) cc_final: 0.3113 (tp) REVERT: G 117 MET cc_start: 0.2761 (mmm) cc_final: 0.2175 (tpp) outliers start: 87 outliers final: 47 residues processed: 442 average time/residue: 0.5240 time to fit residues: 396.4304 Evaluate side-chains 373 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 324 time to evaluate : 5.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 683 GLN Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 469 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 566 ILE Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain Z residue 743 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 455 optimal weight: 9.9990 chunk 310 optimal weight: 0.0770 chunk 7 optimal weight: 9.9990 chunk 407 optimal weight: 50.0000 chunk 225 optimal weight: 3.9990 chunk 466 optimal weight: 10.0000 chunk 378 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 491 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 overall best weight: 4.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN H 29 HIS I 46 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 HIS Z 632 ASN ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 45806 Z= 0.384 Angle : 0.656 11.018 62156 Z= 0.338 Chirality : 0.045 0.203 6784 Planarity : 0.005 0.065 7864 Dihedral : 14.277 164.961 7242 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.63 % Favored : 94.35 % Rotamer: Outliers : 3.12 % Allowed : 12.71 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.12), residues: 5485 helix: 1.21 (0.11), residues: 2231 sheet: -1.19 (0.19), residues: 673 loop : -1.22 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 27 HIS 0.010 0.002 HIS A 839 PHE 0.025 0.002 PHE A 458 TYR 0.033 0.002 TYR B 388 ARG 0.009 0.001 ARG U 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 330 time to evaluate : 5.043 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: B 508 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7184 (mpp) REVERT: B 674 MET cc_start: 0.7926 (tpt) cc_final: 0.7636 (tpt) REVERT: B 1151 MET cc_start: 0.7965 (ptp) cc_final: 0.7682 (ptm) REVERT: U 76 MET cc_start: 0.5528 (mmt) cc_final: 0.5230 (mmp) REVERT: Z 245 LEU cc_start: 0.3703 (OUTLIER) cc_final: 0.3379 (tp) REVERT: Z 254 MET cc_start: 0.0175 (ptp) cc_final: -0.0063 (ptp) outliers start: 138 outliers final: 79 residues processed: 444 average time/residue: 0.5230 time to fit residues: 397.9874 Evaluate side-chains 381 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 300 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 337 PHE Chi-restraints excluded: chain W residue 413 THR Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain Z residue 730 SER Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 184 optimal weight: 2.9990 chunk 492 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 321 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 547 optimal weight: 30.0000 chunk 454 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 287 optimal weight: 0.0050 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN B 420 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN K 69 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN ** U 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 274 HIS ** W 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 45806 Z= 0.158 Angle : 0.556 11.086 62156 Z= 0.285 Chirality : 0.042 0.176 6784 Planarity : 0.003 0.049 7864 Dihedral : 14.161 167.676 7242 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.83 % Allowed : 14.49 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.06 (0.12), residues: 5485 helix: 1.44 (0.12), residues: 2229 sheet: -1.06 (0.19), residues: 700 loop : -1.08 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 203 HIS 0.006 0.001 HIS U 162 PHE 0.027 0.001 PHE A 458 TYR 0.016 0.001 TYR D 67 ARG 0.009 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 321 time to evaluate : 5.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7148 (tpp) REVERT: A 255 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 163 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7869 (pp) REVERT: B 674 MET cc_start: 0.7694 (tpt) cc_final: 0.7455 (tpt) REVERT: B 1151 MET cc_start: 0.8087 (ptp) cc_final: 0.7827 (ptm) REVERT: H 124 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7872 (ttp80) REVERT: Y 42 MET cc_start: 0.1612 (mpp) cc_final: 0.0536 (tmm) REVERT: Z 245 LEU cc_start: 0.3799 (OUTLIER) cc_final: 0.3457 (tp) outliers start: 81 outliers final: 50 residues processed: 391 average time/residue: 0.5274 time to fit residues: 353.1000 Evaluate side-chains 355 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 5.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 575 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain Z residue 743 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 527 optimal weight: 30.0000 chunk 61 optimal weight: 0.9990 chunk 312 optimal weight: 10.0000 chunk 399 optimal weight: 30.0000 chunk 309 optimal weight: 5.9990 chunk 460 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 545 optimal weight: 10.0000 chunk 341 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN A1194 ASN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 HIS ** U 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 188 GLN ** W 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 45806 Z= 0.353 Angle : 0.626 11.861 62156 Z= 0.321 Chirality : 0.044 0.238 6784 Planarity : 0.004 0.058 7864 Dihedral : 14.182 165.337 7242 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.35 % Allowed : 14.38 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.04 (0.12), residues: 5485 helix: 1.40 (0.12), residues: 2252 sheet: -1.03 (0.19), residues: 673 loop : -1.04 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 27 HIS 0.007 0.001 HIS A 839 PHE 0.028 0.002 PHE A 458 TYR 0.023 0.002 TYR B 388 ARG 0.010 0.001 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 304 time to evaluate : 5.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7342 (tpp) REVERT: A 255 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8420 (p) REVERT: A 439 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.6414 (p90) REVERT: A 1428 MET cc_start: 0.7573 (tpp) cc_final: 0.6998 (ttt) REVERT: B 51 ILE cc_start: 0.8595 (tt) cc_final: 0.8352 (tt) REVERT: B 388 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7798 (t80) REVERT: B 674 MET cc_start: 0.7884 (tpt) cc_final: 0.7622 (tpt) REVERT: B 1151 MET cc_start: 0.7993 (ptp) cc_final: 0.7706 (ptm) REVERT: F 94 MET cc_start: 0.6796 (mmm) cc_final: 0.6572 (mmm) REVERT: H 124 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7986 (ttp80) REVERT: U 76 MET cc_start: 0.5677 (mmt) cc_final: 0.5448 (mmt) REVERT: U 125 ARG cc_start: 0.6594 (ttm110) cc_final: 0.6319 (mtm-85) REVERT: Y 64 MET cc_start: 0.1568 (mmm) cc_final: 0.1305 (mmm) REVERT: Z 245 LEU cc_start: 0.4203 (OUTLIER) cc_final: 0.3780 (tp) outliers start: 104 outliers final: 66 residues processed: 389 average time/residue: 0.5298 time to fit residues: 351.1268 Evaluate side-chains 362 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 290 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 575 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 337 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 325 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 346 optimal weight: 0.9980 chunk 371 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 428 optimal weight: 50.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN U 114 ASN ** W 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45806 Z= 0.227 Angle : 0.575 12.324 62156 Z= 0.295 Chirality : 0.042 0.213 6784 Planarity : 0.004 0.049 7864 Dihedral : 14.149 166.146 7242 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.03 % Allowed : 15.17 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.08 (0.12), residues: 5485 helix: 1.54 (0.12), residues: 2240 sheet: -0.96 (0.19), residues: 677 loop : -0.99 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 27 HIS 0.006 0.001 HIS W 462 PHE 0.042 0.001 PHE A 458 TYR 0.017 0.001 TYR E 26 ARG 0.013 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 306 time to evaluate : 5.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8040 (tmm) cc_final: 0.7748 (ttp) REVERT: A 248 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7340 (tpp) REVERT: A 255 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 317 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6900 (tpp) REVERT: A 1428 MET cc_start: 0.7528 (tpp) cc_final: 0.6947 (ttt) REVERT: B 51 ILE cc_start: 0.8516 (tt) cc_final: 0.8243 (tt) REVERT: B 163 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7598 (pp) REVERT: B 388 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7682 (t80) REVERT: B 674 MET cc_start: 0.7801 (tpt) cc_final: 0.7570 (tpt) REVERT: B 1151 MET cc_start: 0.8076 (ptp) cc_final: 0.7824 (ptm) REVERT: H 124 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7958 (ttp80) REVERT: Y 42 MET cc_start: 0.0731 (mpp) cc_final: -0.0294 (tmm) REVERT: Z 245 LEU cc_start: 0.4379 (OUTLIER) cc_final: 0.3884 (tp) outliers start: 90 outliers final: 59 residues processed: 375 average time/residue: 0.5408 time to fit residues: 344.4798 Evaluate side-chains 358 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 292 time to evaluate : 5.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 496 optimal weight: 8.9990 chunk 522 optimal weight: 40.0000 chunk 476 optimal weight: 7.9990 chunk 508 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 399 optimal weight: 50.0000 chunk 156 optimal weight: 5.9990 chunk 459 optimal weight: 8.9990 chunk 480 optimal weight: 6.9990 chunk 506 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN B 913 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 352 HIS ** W 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS G 4 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 45806 Z= 0.417 Angle : 0.668 12.301 62156 Z= 0.341 Chirality : 0.045 0.240 6784 Planarity : 0.004 0.057 7864 Dihedral : 14.234 164.320 7242 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.10 % Allowed : 15.28 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.06 (0.12), residues: 5485 helix: 1.36 (0.11), residues: 2266 sheet: -0.98 (0.19), residues: 667 loop : -1.05 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 27 HIS 0.009 0.001 HIS A 839 PHE 0.028 0.002 PHE A 458 TYR 0.019 0.002 TYR B 388 ARG 0.018 0.001 ARG B 623 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 295 time to evaluate : 5.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7263 (tpp) REVERT: A 255 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 317 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7188 (tpp) REVERT: A 1428 MET cc_start: 0.7601 (tpp) cc_final: 0.7040 (ttt) REVERT: B 51 ILE cc_start: 0.8641 (tt) cc_final: 0.8403 (tt) REVERT: B 388 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7791 (t80) REVERT: B 508 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7285 (mpp) REVERT: B 1151 MET cc_start: 0.8120 (ptp) cc_final: 0.7632 (ptm) REVERT: H 124 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8033 (ttp80) REVERT: U 76 MET cc_start: 0.6360 (mmt) cc_final: 0.6135 (mmt) REVERT: Y 42 MET cc_start: 0.0575 (mpp) cc_final: -0.0318 (tmm) REVERT: Z 254 MET cc_start: 0.0966 (ptm) cc_final: 0.0598 (ptp) outliers start: 93 outliers final: 71 residues processed: 371 average time/residue: 0.5281 time to fit residues: 335.3753 Evaluate side-chains 362 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 285 time to evaluate : 5.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 589 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 333 optimal weight: 3.9990 chunk 537 optimal weight: 2.9990 chunk 328 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 373 optimal weight: 0.0770 chunk 563 optimal weight: 50.0000 chunk 518 optimal weight: 40.0000 chunk 449 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 346 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN B 98 HIS ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45806 Z= 0.184 Angle : 0.586 12.443 62156 Z= 0.297 Chirality : 0.043 0.218 6784 Planarity : 0.004 0.059 7864 Dihedral : 14.167 165.711 7242 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.53 % Allowed : 16.00 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.11 (0.12), residues: 5485 helix: 1.51 (0.12), residues: 2257 sheet: -0.91 (0.19), residues: 669 loop : -0.95 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 203 HIS 0.006 0.001 HIS W 462 PHE 0.016 0.001 PHE W 240 TYR 0.026 0.001 TYR E 26 ARG 0.014 0.000 ARG L 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 305 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7093 (tpp) REVERT: A 1428 MET cc_start: 0.7575 (tpp) cc_final: 0.6999 (ttt) REVERT: B 51 ILE cc_start: 0.8425 (tt) cc_final: 0.8174 (tt) REVERT: B 388 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7629 (t80) REVERT: B 674 MET cc_start: 0.7762 (tpt) cc_final: 0.7534 (tpt) REVERT: B 1151 MET cc_start: 0.8042 (ptp) cc_final: 0.7758 (ptm) REVERT: F 94 MET cc_start: 0.6650 (mmm) cc_final: 0.6364 (mmm) REVERT: H 124 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7950 (ttp80) REVERT: Y 42 MET cc_start: 0.0622 (mpp) cc_final: -0.0275 (tmm) REVERT: Z 245 LEU cc_start: 0.4459 (OUTLIER) cc_final: 0.3958 (tp) REVERT: Z 254 MET cc_start: 0.0848 (ptm) cc_final: 0.0483 (ptp) outliers start: 68 outliers final: 55 residues processed: 363 average time/residue: 0.5395 time to fit residues: 333.8181 Evaluate side-chains 345 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 286 time to evaluate : 5.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 589 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 543 ASP Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 356 optimal weight: 10.0000 chunk 478 optimal weight: 50.0000 chunk 137 optimal weight: 4.9990 chunk 414 optimal weight: 50.0000 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 449 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 461 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.118700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075224 restraints weight = 115142.394| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.08 r_work: 0.2965 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45806 Z= 0.211 Angle : 0.585 12.869 62156 Z= 0.295 Chirality : 0.042 0.215 6784 Planarity : 0.003 0.050 7864 Dihedral : 14.103 165.392 7242 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.56 % Allowed : 15.98 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.12), residues: 5485 helix: 1.59 (0.12), residues: 2258 sheet: -0.87 (0.19), residues: 674 loop : -0.92 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 27 HIS 0.005 0.001 HIS W 462 PHE 0.014 0.001 PHE A 592 TYR 0.025 0.001 TYR E 26 ARG 0.009 0.000 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10259.26 seconds wall clock time: 192 minutes 16.51 seconds (11536.51 seconds total)