Starting phenix.real_space_refine on Mon Mar 25 07:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f40_4180/03_2024/6f40_4180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f40_4180/03_2024/6f40_4180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f40_4180/03_2024/6f40_4180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f40_4180/03_2024/6f40_4180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f40_4180/03_2024/6f40_4180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f40_4180/03_2024/6f40_4180.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 113 5.49 5 S 242 5.16 5 C 29690 2.51 5 N 8205 2.21 5 O 9139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1068": "NH1" <-> "NH2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 874": "NH1" <-> "NH2" Residue "B PHE 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1054": "NH1" <-> "NH2" Residue "B TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 93": "NH1" <-> "NH2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 199": "NH1" <-> "NH2" Residue "N ARG 411": "NH1" <-> "NH2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 291": "NH1" <-> "NH2" Residue "O ARG 292": "NH1" <-> "NH2" Residue "O ARG 327": "NH1" <-> "NH2" Residue "O ARG 557": "NH1" <-> "NH2" Residue "O ARG 561": "NH1" <-> "NH2" Residue "O ARG 640": "NH1" <-> "NH2" Residue "O ARG 643": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 113": "NH1" <-> "NH2" Residue "P ARG 145": "NH1" <-> "NH2" Residue "P ARG 184": "NH1" <-> "NH2" Residue "P ARG 262": "NH1" <-> "NH2" Residue "U ARG 98": "NH1" <-> "NH2" Residue "V ARG 14": "NH1" <-> "NH2" Residue "V ARG 208": "NH1" <-> "NH2" Residue "V ARG 219": "NH1" <-> "NH2" Residue "V ARG 294": "NH1" <-> "NH2" Residue "W ARG 307": "NH1" <-> "NH2" Residue "W ARG 308": "NH1" <-> "NH2" Residue "W ARG 311": "NH1" <-> "NH2" Residue "W ARG 314": "NH1" <-> "NH2" Residue "W ARG 316": "NH1" <-> "NH2" Residue "W ARG 318": "NH1" <-> "NH2" Residue "W TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 413": "NH1" <-> "NH2" Residue "W ARG 449": "NH1" <-> "NH2" Residue "W ARG 451": "NH1" <-> "NH2" Residue "W ARG 474": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47396 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 10972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10972 Classifications: {'peptide': 1398} Link IDs: {'PTRANS': 65, 'TRANS': 1332} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 43, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1448 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 255 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1484 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain breaks: 1 Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "O" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4293 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 18, 'TRANS': 515} Chain breaks: 2 Chain: "P" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1990 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 4, 'TRANS': 241} Chain breaks: 3 Chain: "Q" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 273 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 5, 'TRANS': 29} Chain: "U" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Chain: "V" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2686 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 326} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1798 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1137 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "Y" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1179 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "V" 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 491 SG CYS A 67 88.648 76.047 82.367 1.00 66.88 S ATOM 509 SG CYS A 70 91.472 76.722 79.783 1.00 67.06 S ATOM 794 SG CYS A 107 73.738 122.457 93.766 1.00 59.93 S ATOM 817 SG CYS A 110 72.926 122.840 89.820 1.00 66.10 S ATOM 1183 SG CYS A 154 73.486 125.804 92.515 1.00 69.49 S ATOM 1207 SG CYS A 157 70.305 124.521 92.034 1.00 75.25 S ATOM 19333 SG CYS B1095 94.273 92.635 72.766 1.00 57.44 S ATOM 19356 SG CYS B1098 90.942 95.526 74.620 1.00 58.95 S ATOM 19422 SG CYS B1107 91.357 90.989 74.741 1.00 56.24 S ATOM 19442 SG CYS B1110 90.254 93.095 72.171 1.00 63.07 S ATOM 28421 SG CYS I 5 80.911 127.394 159.133 1.00 53.97 S ATOM 28440 SG CYS I 8 80.315 123.951 158.814 1.00 55.00 S ATOM 28568 SG CYS I 26 79.529 127.719 155.830 1.00 59.36 S ATOM 28591 SG CYS I 29 77.344 126.387 159.545 1.00 59.83 S ATOM 28691 SG CYS J 7 140.671 52.483 127.292 1.00 35.68 S ATOM 28714 SG CYS J 10 144.041 51.124 126.474 1.00 33.11 S ATOM 28994 SG CYS J 45 144.215 54.430 128.723 1.00 41.31 S ATOM 29000 SG CYS J 46 143.275 50.734 130.054 1.00 40.20 S ATOM 30152 SG CYS L 48 95.554 37.674 126.305 1.00 44.89 S ATOM 40609 SG CYS V 4 104.782 57.871 76.447 1.00 80.02 S ATOM 40632 SG CYS V 7 105.180 54.138 76.598 1.00 80.49 S ATOM 40773 SG CYS V 25 106.515 55.138 79.884 1.00 71.99 S ATOM 40793 SG CYS V 28 108.333 56.160 76.988 1.00 71.55 S Time building chain proxies: 25.63, per 1000 atoms: 0.54 Number of scatterers: 47396 At special positions: 0 Unit cell: (203.85, 174.15, 206.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 242 16.00 P 113 15.00 O 9139 8.00 N 8205 7.00 C 29690 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: 17.42 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 29 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb=" ZN L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 25 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 4 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 7 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 28 " Number of angles added : 30 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10736 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 0 sheets defined 37.0% alpha, 0.0% beta 36 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 15.02 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.661A pdb=" N THR A 99 " --> pdb=" O PHE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.636A pdb=" N LYS A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.737A pdb=" N MET A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.599A pdb=" N ASP A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.528A pdb=" N LYS A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 206 removed outlier: 3.514A pdb=" N ALA A 206 " --> pdb=" O GLU A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.614A pdb=" N LEU A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 215 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.759A pdb=" N LEU A 241 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 removed outlier: 4.133A pdb=" N ARG A 252 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 283 through 306 removed outlier: 3.943A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 removed outlier: 4.801A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 320 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.731A pdb=" N SER A 331 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 333 " --> pdb=" O ASP A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 333' Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.869A pdb=" N LYS A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.529A pdb=" N LYS A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 400' Processing helix chain 'A' and resid 412 through 421 removed outlier: 4.089A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.877A pdb=" N THR A 506 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 removed outlier: 3.521A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 676 through 704 removed outlier: 3.637A pdb=" N THR A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 681 " --> pdb=" O VAL A 677 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Proline residue: A 687 - end of helix removed outlier: 3.764A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 698 " --> pdb=" O MET A 694 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.526A pdb=" N ASP A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 3.544A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 removed outlier: 3.835A pdb=" N GLU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 784 removed outlier: 4.967A pdb=" N ILE A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 767 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.543A pdb=" N MET A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 811 Processing helix chain 'A' and resid 857 through 874 removed outlier: 4.179A pdb=" N LEU A 862 " --> pdb=" O PRO A 858 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 892 removed outlier: 3.615A pdb=" N LYS A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.535A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 973 removed outlier: 4.177A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Proline residue: A 969 - end of helix removed outlier: 3.708A pdb=" N GLU A 972 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1026 removed outlier: 3.671A pdb=" N TYR A1005 " --> pdb=" O GLU A1001 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS A1006 " --> pdb=" O ARG A1002 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 removed outlier: 4.024A pdb=" N LYS A1053 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A1057 " --> pdb=" O LYS A1053 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN A1058 " --> pdb=" O THR A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1069 Processing helix chain 'A' and resid 1069 through 1081 removed outlier: 3.616A pdb=" N ILE A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1098 removed outlier: 3.743A pdb=" N GLN A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 5.125A pdb=" N GLU A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A1129 " --> pdb=" O ARG A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 4.031A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1194 " --> pdb=" O LEU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1211 removed outlier: 3.853A pdb=" N ALA A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 4.227A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A1260 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A1261 " --> pdb=" O PHE A1257 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1263 " --> pdb=" O ARG A1259 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A1264 " --> pdb=" O MET A1260 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A1265 " --> pdb=" O GLN A1261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A1266 " --> pdb=" O GLN A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1306 Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.931A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1340 removed outlier: 3.525A pdb=" N ILE A1336 " --> pdb=" O ARG A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1363 removed outlier: 4.092A pdb=" N LEU A1358 " --> pdb=" O HIS A1354 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP A1360 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A1363 " --> pdb=" O GLY A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1377 removed outlier: 3.634A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1388 removed outlier: 3.804A pdb=" N SER A1388 " --> pdb=" O LEU A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1403 removed outlier: 3.662A pdb=" N LEU A1396 " --> pdb=" O THR A1392 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP A1398 " --> pdb=" O ASP A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1414 removed outlier: 3.569A pdb=" N GLU A1413 " --> pdb=" O GLY A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1441 removed outlier: 4.199A pdb=" N ASP A1440 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.525A pdb=" N LEU B 47 " --> pdb=" O LYS B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 48 through 55 removed outlier: 4.299A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 4.261A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.631A pdb=" N LYS B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 278 through 284 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.936A pdb=" N LEU B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.787A pdb=" N GLY B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.585A pdb=" N ALA B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 347 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 383 through 396 removed outlier: 3.651A pdb=" N LEU B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 3.640A pdb=" N ASP B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 removed outlier: 3.530A pdb=" N SER B 421 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 422 " --> pdb=" O LEU B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 422' Processing helix chain 'B' and resid 426 through 439 removed outlier: 3.856A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.715A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 536 removed outlier: 3.773A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 581 removed outlier: 3.755A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 581 " --> pdb=" O HIS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.563A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 removed outlier: 3.685A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.958A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 4.105A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 removed outlier: 3.974A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 818 through 822 removed outlier: 4.071A pdb=" N GLN B 822 " --> pdb=" O TRP B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 953 Processing helix chain 'B' and resid 955 through 971 removed outlier: 3.908A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 994 removed outlier: 3.528A pdb=" N LEU B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1034 removed outlier: 3.887A pdb=" N ASP B1033 " --> pdb=" O MET B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1072 removed outlier: 3.528A pdb=" N ASP B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1084 removed outlier: 3.512A pdb=" N LEU B1083 " --> pdb=" O LEU B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1127 Processing helix chain 'B' and resid 1127 through 1135 removed outlier: 4.016A pdb=" N LEU B1133 " --> pdb=" O PHE B1129 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 removed outlier: 3.613A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.594A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 71 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 removed outlier: 3.711A pdb=" N HIS C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.639A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 309 through 327 removed outlier: 3.835A pdb=" N ILE C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 removed outlier: 3.765A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 72 removed outlier: 3.891A pdb=" N ILE D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 removed outlier: 3.856A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 123 removed outlier: 4.221A pdb=" N GLN D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 118 through 123' Processing helix chain 'D' and resid 133 through 138 removed outlier: 4.095A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'E' and resid 3 through 27 removed outlier: 3.815A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.789A pdb=" N PHE E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.722A pdb=" N LYS E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.864A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE E 100 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 4.125A pdb=" N MET E 121 " --> pdb=" O PRO E 118 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS E 122 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 157 through 162 removed outlier: 3.915A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.910A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 102 removed outlier: 3.751A pdb=" N LEU F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 125 removed outlier: 3.578A pdb=" N LYS F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.723A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.640A pdb=" N HIS G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS G 33 " --> pdb=" O GLN G 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 20 No H-bonds generated for 'chain 'I' and resid 18 through 20' Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.746A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 4.197A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG J 38 " --> pdb=" O THR J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.588A pdb=" N LEU J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 50 through 54 removed outlier: 3.826A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 Processing helix chain 'K' and resid 74 through 81 removed outlier: 3.574A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 124 removed outlier: 3.802A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS K 122 " --> pdb=" O GLN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 142 removed outlier: 3.728A pdb=" N ASP K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 131 Processing helix chain 'M' and resid 132 through 141 removed outlier: 3.808A pdb=" N SER M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 201 removed outlier: 3.940A pdb=" N ASN M 190 " --> pdb=" O ILE M 186 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 238 removed outlier: 3.528A pdb=" N ALA M 233 " --> pdb=" O GLY M 229 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS M 234 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP M 238 " --> pdb=" O HIS M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 261 removed outlier: 3.597A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS M 261 " --> pdb=" O ASP M 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 296 removed outlier: 3.812A pdb=" N GLU N 281 " --> pdb=" O ALA N 277 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU N 282 " --> pdb=" O ALA N 278 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS N 289 " --> pdb=" O ALA N 285 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG N 292 " --> pdb=" O GLN N 288 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS N 293 " --> pdb=" O HIS N 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.919A pdb=" N THR O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU O 42 " --> pdb=" O GLU O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 42' Processing helix chain 'O' and resid 45 through 56 removed outlier: 4.028A pdb=" N GLU O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 61 through 72 removed outlier: 3.561A pdb=" N MET O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 83 removed outlier: 3.630A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.888A pdb=" N SER O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 132 through 142 removed outlier: 4.365A pdb=" N ILE O 137 " --> pdb=" O SER O 133 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP O 138 " --> pdb=" O GLY O 134 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE O 141 " --> pdb=" O ILE O 137 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 164 removed outlier: 3.983A pdb=" N GLU O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL O 160 " --> pdb=" O VAL O 156 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN O 161 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE O 164 " --> pdb=" O VAL O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 176 removed outlier: 3.734A pdb=" N LEU O 175 " --> pdb=" O VAL O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 196 removed outlier: 3.508A pdb=" N ILE O 187 " --> pdb=" O MET O 183 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE O 191 " --> pdb=" O ILE O 187 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 226 removed outlier: 4.825A pdb=" N PHE O 217 " --> pdb=" O ASP O 213 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE O 226 " --> pdb=" O HIS O 222 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 253 removed outlier: 4.030A pdb=" N ALA O 241 " --> pdb=" O LYS O 237 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS O 242 " --> pdb=" O ARG O 238 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN O 244 " --> pdb=" O GLN O 240 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 258 removed outlier: 4.102A pdb=" N ASN O 257 " --> pdb=" O ILE O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 304 removed outlier: 4.242A pdb=" N ASN O 298 " --> pdb=" O LYS O 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU O 299 " --> pdb=" O GLN O 295 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA O 300 " --> pdb=" O LEU O 296 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 319 removed outlier: 3.739A pdb=" N LYS O 313 " --> pdb=" O ALA O 309 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA O 315 " --> pdb=" O VAL O 311 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR O 319 " --> pdb=" O ALA O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 343 Processing helix chain 'O' and resid 343 through 355 removed outlier: 3.731A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA O 349 " --> pdb=" O PHE O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 365 through 370 removed outlier: 3.898A pdb=" N HIS O 369 " --> pdb=" O ASP O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 463 removed outlier: 3.524A pdb=" N LEU O 457 " --> pdb=" O ILE O 453 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE O 459 " --> pdb=" O SER O 455 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU O 460 " --> pdb=" O HIS O 456 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA O 461 " --> pdb=" O LEU O 457 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 500 removed outlier: 3.781A pdb=" N SER O 489 " --> pdb=" O PRO O 485 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU O 493 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.819A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP O 513 " --> pdb=" O ARG O 509 " (cutoff:3.500A) Processing helix chain 'O' and resid 520 through 526 Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.919A pdb=" N ARG O 534 " --> pdb=" O GLU O 530 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER O 535 " --> pdb=" O LYS O 531 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER O 539 " --> pdb=" O SER O 535 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU O 540 " --> pdb=" O THR O 536 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 594 removed outlier: 3.511A pdb=" N PHE O 576 " --> pdb=" O HIS O 572 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET O 577 " --> pdb=" O SER O 573 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU O 581 " --> pdb=" O MET O 577 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN O 584 " --> pdb=" O ASN O 580 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU O 593 " --> pdb=" O LEU O 589 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS O 594 " --> pdb=" O PHE O 590 " (cutoff:3.500A) Processing helix chain 'O' and resid 624 through 629 Processing helix chain 'O' and resid 634 through 649 removed outlier: 3.899A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA O 639 " --> pdb=" O LEU O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 650 through 653 removed outlier: 3.739A pdb=" N MET O 653 " --> pdb=" O VAL O 650 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 650 through 653' Processing helix chain 'P' and resid 12 through 25 removed outlier: 3.663A pdb=" N SER P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN P 21 " --> pdb=" O THR P 17 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS P 25 " --> pdb=" O GLN P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 40 removed outlier: 3.914A pdb=" N LYS P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 58 removed outlier: 4.463A pdb=" N SER P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 51 " --> pdb=" O ASP P 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 85 removed outlier: 3.604A pdb=" N LYS P 83 " --> pdb=" O GLU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 101 removed outlier: 3.924A pdb=" N TYR P 96 " --> pdb=" O LEU P 92 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY P 101 " --> pdb=" O ILE P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 113 Processing helix chain 'P' and resid 117 through 131 removed outlier: 3.671A pdb=" N CYS P 124 " --> pdb=" O VAL P 120 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS P 126 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER P 127 " --> pdb=" O LYS P 123 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER P 130 " --> pdb=" O LYS P 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN P 131 " --> pdb=" O SER P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 188 removed outlier: 3.875A pdb=" N LEU P 179 " --> pdb=" O ILE P 175 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU P 188 " --> pdb=" O ARG P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 227 removed outlier: 4.411A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE P 224 " --> pdb=" O GLU P 220 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE P 225 " --> pdb=" O ILE P 221 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA P 227 " --> pdb=" O GLU P 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 250 removed outlier: 3.617A pdb=" N SER P 242 " --> pdb=" O SER P 238 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL P 246 " --> pdb=" O SER P 242 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU P 247 " --> pdb=" O LEU P 243 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR P 249 " --> pdb=" O GLU P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 271 Processing helix chain 'Q' and resid 48 through 53 removed outlier: 3.949A pdb=" N SER Q 53 " --> pdb=" O ASN Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 67 removed outlier: 3.944A pdb=" N ILE Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN Q 60 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 87 removed outlier: 3.539A pdb=" N ALA U 86 " --> pdb=" O LEU U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 144 removed outlier: 3.579A pdb=" N LEU U 134 " --> pdb=" O ASP U 130 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA U 140 " --> pdb=" O SER U 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE U 142 " --> pdb=" O LYS U 138 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE U 143 " --> pdb=" O TYR U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 179 removed outlier: 3.541A pdb=" N ALA U 176 " --> pdb=" O LEU U 172 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 222 No H-bonds generated for 'chain 'U' and resid 220 through 222' Processing helix chain 'U' and resid 223 through 230 removed outlier: 3.777A pdb=" N GLU U 228 " --> pdb=" O TYR U 224 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 236 removed outlier: 3.929A pdb=" N SER U 235 " --> pdb=" O TYR U 231 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU U 236 " --> pdb=" O PRO U 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 231 through 236' Processing helix chain 'V' and resid 74 through 94 removed outlier: 3.712A pdb=" N LEU V 80 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA V 83 " --> pdb=" O THR V 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG V 85 " --> pdb=" O ASN V 81 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU V 87 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 114 removed outlier: 4.094A pdb=" N THR V 101 " --> pdb=" O PRO V 97 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP V 102 " --> pdb=" O GLU V 98 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA V 103 " --> pdb=" O TYR V 99 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN V 106 " --> pdb=" O ASP V 102 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TRP V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 137 removed outlier: 3.648A pdb=" N ILE V 126 " --> pdb=" O SER V 122 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA V 127 " --> pdb=" O GLN V 123 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER V 128 " --> pdb=" O ASN V 124 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL V 132 " --> pdb=" O SER V 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA V 133 " --> pdb=" O CYS V 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU V 137 " --> pdb=" O ALA V 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 151 removed outlier: 3.778A pdb=" N SER V 147 " --> pdb=" O LEU V 143 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG V 149 " --> pdb=" O ASP V 145 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU V 150 " --> pdb=" O PHE V 146 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 166 removed outlier: 3.683A pdb=" N ILE V 157 " --> pdb=" O SER V 153 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR V 160 " --> pdb=" O SER V 156 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET V 164 " --> pdb=" O THR V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 190 removed outlier: 4.017A pdb=" N ILE V 182 " --> pdb=" O PRO V 178 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN V 183 " --> pdb=" O SER V 179 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS V 184 " --> pdb=" O LEU V 180 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA V 186 " --> pdb=" O ILE V 182 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLU V 187 " --> pdb=" O GLN V 183 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS V 188 " --> pdb=" O HIS V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 196 through 212 removed outlier: 3.881A pdb=" N ALA V 202 " --> pdb=" O VAL V 198 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS V 204 " --> pdb=" O LYS V 200 " (cutoff:3.500A) Processing helix chain 'V' and resid 219 through 224 removed outlier: 3.527A pdb=" N ALA V 224 " --> pdb=" O PRO V 220 " (cutoff:3.500A) Processing helix chain 'V' and resid 226 through 232 Processing helix chain 'V' and resid 244 through 249 Processing helix chain 'V' and resid 252 through 264 removed outlier: 3.820A pdb=" N GLN V 256 " --> pdb=" O GLU V 252 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG V 258 " --> pdb=" O THR V 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS V 263 " --> pdb=" O LEU V 259 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN V 264 " --> pdb=" O ASN V 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 287 through 292 removed outlier: 3.685A pdb=" N VAL V 291 " --> pdb=" O PRO V 287 " (cutoff:3.500A) Processing helix chain 'V' and resid 292 through 297 removed outlier: 3.908A pdb=" N GLU V 297 " --> pdb=" O ASN V 293 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 453 removed outlier: 3.675A pdb=" N SER V 453 " --> pdb=" O ASP V 449 " (cutoff:3.500A) Processing helix chain 'V' and resid 479 through 490 removed outlier: 3.726A pdb=" N LYS V 483 " --> pdb=" O ALA V 479 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE V 486 " --> pdb=" O LEU V 482 " (cutoff:3.500A) Processing helix chain 'V' and resid 492 through 510 removed outlier: 3.518A pdb=" N SER V 500 " --> pdb=" O LEU V 496 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE V 509 " --> pdb=" O GLN V 505 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 319 removed outlier: 3.560A pdb=" N LYS W 300 " --> pdb=" O SER W 296 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU W 304 " --> pdb=" O LYS W 300 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU W 305 " --> pdb=" O LYS W 301 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS W 306 " --> pdb=" O ALA W 302 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU W 310 " --> pdb=" O LYS W 306 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG W 311 " --> pdb=" O ARG W 307 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET W 315 " --> pdb=" O ARG W 311 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG W 316 " --> pdb=" O GLU W 312 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN W 319 " --> pdb=" O MET W 315 " (cutoff:3.500A) Processing helix chain 'W' and resid 384 through 393 removed outlier: 3.761A pdb=" N GLU W 390 " --> pdb=" O ASN W 386 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR W 393 " --> pdb=" O ILE W 389 " (cutoff:3.500A) Processing helix chain 'W' and resid 421 through 426 removed outlier: 3.706A pdb=" N ILE W 426 " --> pdb=" O VAL W 422 " (cutoff:3.500A) Processing helix chain 'W' and resid 428 through 435 Processing helix chain 'W' and resid 438 through 446 removed outlier: 3.772A pdb=" N ILE W 442 " --> pdb=" O ASP W 438 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN W 444 " --> pdb=" O ASN W 440 " (cutoff:3.500A) Processing helix chain 'W' and resid 450 through 465 removed outlier: 3.851A pdb=" N VAL W 454 " --> pdb=" O SER W 450 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS W 455 " --> pdb=" O ARG W 451 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU W 462 " --> pdb=" O PHE W 458 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS W 463 " --> pdb=" O VAL W 459 " (cutoff:3.500A) Processing helix chain 'W' and resid 467 through 475 Processing helix chain 'W' and resid 482 through 492 removed outlier: 4.419A pdb=" N CYS W 486 " --> pdb=" O ASP W 482 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS W 490 " --> pdb=" O CYS W 486 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN W 491 " --> pdb=" O GLU W 487 " (cutoff:3.500A) Processing helix chain 'W' and resid 497 through 537 removed outlier: 3.650A pdb=" N LEU W 502 " --> pdb=" O PHE W 498 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE W 503 " --> pdb=" O ASN W 499 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU W 505 " --> pdb=" O LYS W 501 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN W 506 " --> pdb=" O LEU W 502 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU W 518 " --> pdb=" O LYS W 514 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA W 523 " --> pdb=" O ALA W 519 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP W 527 " --> pdb=" O ALA W 523 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN W 528 " --> pdb=" O LYS W 524 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA W 530 " --> pdb=" O GLU W 526 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP W 535 " --> pdb=" O GLN W 531 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 15.20 Time building geometry restraints manager: 18.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14942 1.34 - 1.46: 6928 1.46 - 1.58: 25983 1.58 - 1.69: 222 1.69 - 1.81: 392 Bond restraints: 48467 Sorted by residual: bond pdb=" N LYS P 298 " pdb=" CA LYS P 298 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.57e+00 bond pdb=" CA ASN B 814 " pdb=" CB ASN B 814 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.54e+00 bond pdb=" C LEU A1267 " pdb=" N PRO A1268 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.29e+00 bond pdb=" CA PHE B 477 " pdb=" CB PHE B 477 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.21e+00 bond pdb=" CA PHE B 567 " pdb=" CB PHE B 567 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.58e-02 4.01e+03 1.19e+00 ... (remaining 48462 not shown) Histogram of bond angle deviations from ideal: 98.43 - 106.43: 1963 106.43 - 114.43: 28737 114.43 - 122.43: 27966 122.43 - 130.43: 7029 130.43 - 138.43: 197 Bond angle restraints: 65892 Sorted by residual: angle pdb=" C VAL B 187 " pdb=" N ASN B 188 " pdb=" CA ASN B 188 " ideal model delta sigma weight residual 121.54 129.50 -7.96 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C PRO C 110 " pdb=" N ASP C 111 " pdb=" CA ASP C 111 " ideal model delta sigma weight residual 126.45 133.34 -6.89 1.77e+00 3.19e-01 1.51e+01 angle pdb=" C CYS A 70 " pdb=" N HIS A 71 " pdb=" CA HIS A 71 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C ILE A 389 " pdb=" N ASP A 390 " pdb=" CA ASP A 390 " ideal model delta sigma weight residual 125.66 132.51 -6.85 1.85e+00 2.92e-01 1.37e+01 angle pdb=" C LYS H 109 " pdb=" N ASP H 110 " pdb=" CA ASP H 110 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 ... (remaining 65887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 28666 35.10 - 70.21: 813 70.21 - 105.31: 32 105.31 - 140.41: 1 140.41 - 175.52: 2 Dihedral angle restraints: 29514 sinusoidal: 12959 harmonic: 16555 Sorted by residual: dihedral pdb=" CA CYS A 70 " pdb=" C CYS A 70 " pdb=" N HIS A 71 " pdb=" CA HIS A 71 " ideal model delta harmonic sigma weight residual 180.00 133.19 46.81 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CA ASP B1057 " pdb=" C ASP B1057 " pdb=" N GLY B1058 " pdb=" CA GLY B1058 " ideal model delta harmonic sigma weight residual 180.00 149.01 30.99 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA GLN W 288 " pdb=" C GLN W 288 " pdb=" N ILE W 289 " pdb=" CA ILE W 289 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 29511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 6044 0.052 - 0.104: 1209 0.104 - 0.156: 182 0.156 - 0.209: 10 0.209 - 0.261: 1 Chirality restraints: 7446 Sorted by residual: chirality pdb=" CB ILE E 127 " pdb=" CA ILE E 127 " pdb=" CG1 ILE E 127 " pdb=" CG2 ILE E 127 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASP B 816 " pdb=" N ASP B 816 " pdb=" C ASP B 816 " pdb=" CB ASP B 816 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CA ASN B 188 " pdb=" N ASN B 188 " pdb=" C ASN B 188 " pdb=" CB ASN B 188 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 7443 not shown) Planarity restraints: 8071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1351 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A1352 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A1352 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1352 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 949 " 0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO B 950 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 950 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 950 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 610 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO B 611 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 611 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 611 " -0.035 5.00e-02 4.00e+02 ... (remaining 8068 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1804 2.71 - 3.26: 47416 3.26 - 3.81: 72480 3.81 - 4.35: 92973 4.35 - 4.90: 148290 Nonbonded interactions: 362963 Sorted by model distance: nonbonded pdb=" OD2 ASP G 63 " pdb=" OH TYR G 67 " model vdw 2.166 2.440 nonbonded pdb=" OD2 ASP A 181 " pdb=" NH1 ARG A 184 " model vdw 2.213 2.520 nonbonded pdb=" O VAL O 352 " pdb=" OG1 THR O 356 " model vdw 2.225 2.440 nonbonded pdb=" NH1 ARG A 464 " pdb=" OE2 GLU A 467 " model vdw 2.231 2.520 nonbonded pdb=" N CYS A 70 " pdb="ZN ZN A1501 " model vdw 2.234 2.310 ... (remaining 362958 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 6.360 Check model and map are aligned: 0.750 Set scattering table: 0.450 Process input model: 134.480 Find NCS groups from input model: 1.300 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 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 : 0.002 0.033 48467 Z= 0.124 Angle : 0.639 17.719 65892 Z= 0.348 Chirality : 0.042 0.261 7446 Planarity : 0.006 0.074 8071 Dihedral : 14.925 175.517 18778 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.93 % Favored : 89.01 % Rotamer: Outliers : 0.84 % Allowed : 8.83 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.08), residues: 5589 helix: -4.39 (0.06), residues: 1749 sheet: -2.94 (0.19), residues: 569 loop : -3.10 (0.09), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP P 106 HIS 0.009 0.001 HIS A 71 PHE 0.029 0.001 PHE B 567 TYR 0.016 0.001 TYR B 125 ARG 0.016 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 959 time to evaluate : 5.478 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: A 273 MET cc_start: 0.5751 (tpp) cc_final: 0.5373 (mmm) REVERT: A 281 ASN cc_start: 0.7680 (t0) cc_final: 0.7353 (p0) REVERT: A 321 LEU cc_start: 0.9127 (tm) cc_final: 0.8805 (tt) REVERT: A 582 MET cc_start: 0.8943 (mtm) cc_final: 0.8552 (mtp) REVERT: A 744 LEU cc_start: 0.4211 (OUTLIER) cc_final: 0.3910 (mt) REVERT: A 866 ILE cc_start: 0.8048 (mm) cc_final: 0.7648 (mt) REVERT: A 990 ASN cc_start: 0.8878 (p0) cc_final: 0.8599 (p0) REVERT: A 1183 PHE cc_start: 0.7263 (p90) cc_final: 0.6917 (p90) REVERT: A 1302 ASP cc_start: 0.8351 (p0) cc_final: 0.7702 (p0) REVERT: A 1320 LEU cc_start: 0.8230 (pt) cc_final: 0.8001 (tt) REVERT: A 1398 ASP cc_start: 0.7049 (p0) cc_final: 0.6805 (p0) REVERT: B 296 TYR cc_start: 0.7608 (m-10) cc_final: 0.7330 (m-80) REVERT: B 412 ARG cc_start: 0.7157 (mmm160) cc_final: 0.6880 (mmm160) REVERT: B 544 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7759 (pt) REVERT: B 565 ILE cc_start: 0.8212 (tp) cc_final: 0.7966 (tp) REVERT: B 648 TYR cc_start: 0.8797 (m-80) cc_final: 0.8533 (m-80) REVERT: B 670 MET cc_start: 0.7403 (tpp) cc_final: 0.6852 (tpp) REVERT: B 944 MET cc_start: 0.6969 (ptm) cc_final: 0.6746 (ptm) REVERT: B 1024 TYR cc_start: 0.8449 (m-10) cc_final: 0.7524 (m-80) REVERT: B 1119 MET cc_start: 0.7433 (mtm) cc_final: 0.7159 (ptp) REVERT: C 142 ARG cc_start: 0.7863 (tpp80) cc_final: 0.7651 (mtt-85) REVERT: C 166 ASP cc_start: 0.8430 (m-30) cc_final: 0.8172 (m-30) REVERT: C 209 ILE cc_start: 0.9168 (pt) cc_final: 0.8830 (tt) REVERT: C 327 TYR cc_start: 0.8899 (t80) cc_final: 0.8642 (t80) REVERT: D 55 LEU cc_start: 0.4812 (pt) cc_final: 0.4494 (mt) REVERT: E 57 MET cc_start: 0.6265 (tmm) cc_final: 0.5833 (mmm) REVERT: E 93 MET cc_start: 0.6113 (pmt) cc_final: 0.5139 (ptt) REVERT: E 112 TYR cc_start: 0.7108 (t80) cc_final: 0.6707 (t80) REVERT: F 119 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7450 (mtm-85) REVERT: F 130 ILE cc_start: 0.9276 (mm) cc_final: 0.8903 (mm) REVERT: G 41 ASN cc_start: 0.7392 (m110) cc_final: 0.6617 (t0) REVERT: G 124 GLU cc_start: 0.5453 (tm-30) cc_final: 0.5236 (pp20) REVERT: H 141 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: I 10 ASN cc_start: 0.7743 (t0) cc_final: 0.7073 (t0) REVERT: I 15 THR cc_start: 0.7205 (m) cc_final: 0.6692 (p) REVERT: K 92 SER cc_start: 0.8923 (t) cc_final: 0.8385 (p) REVERT: K 112 THR cc_start: 0.8989 (p) cc_final: 0.8680 (t) REVERT: K 126 ASP cc_start: 0.8368 (m-30) cc_final: 0.8103 (m-30) REVERT: L 36 SER cc_start: 0.8631 (m) cc_final: 0.8383 (m) REVERT: L 47 ARG cc_start: 0.8383 (ptp-110) cc_final: 0.8115 (mtm110) REVERT: N 274 LYS cc_start: 0.5306 (mttm) cc_final: 0.4672 (mmtt) REVERT: N 286 ASP cc_start: 0.7073 (t0) cc_final: 0.6607 (t0) REVERT: N 416 ILE cc_start: 0.8019 (pp) cc_final: 0.7367 (pt) REVERT: O 77 ARG cc_start: 0.6749 (mmt-90) cc_final: 0.6456 (mpt180) REVERT: O 583 TRP cc_start: 0.8264 (t60) cc_final: 0.8032 (t60) REVERT: P 14 ASN cc_start: 0.6336 (t0) cc_final: 0.5442 (p0) REVERT: P 40 MET cc_start: 0.6860 (mmm) cc_final: 0.6307 (tmm) REVERT: P 55 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.5071 (tt) REVERT: P 174 PHE cc_start: 0.3513 (m-10) cc_final: 0.3276 (m-10) REVERT: Q 51 GLU cc_start: 0.6982 (pm20) cc_final: 0.6732 (pm20) REVERT: V 262 PHE cc_start: 0.6985 (t80) cc_final: 0.6778 (t80) REVERT: V 292 LYS cc_start: 0.7131 (mmpt) cc_final: 0.6892 (mttm) REVERT: V 478 GLU cc_start: 0.7341 (pm20) cc_final: 0.6427 (pp20) REVERT: W 316 ARG cc_start: 0.6714 (ptm-80) cc_final: 0.6485 (ptm160) outliers start: 42 outliers final: 8 residues processed: 994 average time/residue: 0.6275 time to fit residues: 998.3819 Evaluate side-chains 540 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 528 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 479 optimal weight: 9.9990 chunk 430 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 290 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 445 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 515 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 488 HIS A 520 HIS A 540 ASN A 578 GLN A 618 HIS A 688 GLN A 715 ASN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 HIS A1346 HIS A1354 HIS A1419 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 270 GLN B 574 GLN B 577 HIS B 600 HIS B 753 GLN B 859 ASN B 893 GLN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 ASN C 87 ASN C 175 GLN C 207 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 113 ASN H 139 ASN K 74 ASN M 117 HIS M 128 GLN M 144 ASN M 220 ASN M 254 GLN O 225 ASN O 332 GLN O 523 ASN O 549 GLN O 572 HIS O 631 ASN O 636 ASN P 59 ASN P 119 HIS P 189 ASN U 91 ASN U 159 ASN V 6 ASN V 20 ASN V 35 ASN V 115 ASN ** V 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 249 HIS V 473 HIS ** W 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 292 ASN W 404 ASN ** W 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 521 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 48467 Z= 0.290 Angle : 0.723 18.030 65892 Z= 0.372 Chirality : 0.046 0.286 7446 Planarity : 0.005 0.070 8071 Dihedral : 15.606 179.640 7425 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 3.27 % Allowed : 13.08 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -4.33 (0.09), residues: 5589 helix: -3.14 (0.09), residues: 1905 sheet: -2.44 (0.19), residues: 612 loop : -2.83 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 185 HIS 0.010 0.001 HIS W 309 PHE 0.026 0.002 PHE H 6 TYR 0.032 0.002 TYR O 208 ARG 0.012 0.001 ARG W 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 549 time to evaluate : 5.267 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 219 MET cc_start: 0.7125 (tpp) cc_final: 0.6628 (mtp) REVERT: A 273 MET cc_start: 0.5927 (tpp) cc_final: 0.5393 (mmm) REVERT: A 281 ASN cc_start: 0.7718 (t0) cc_final: 0.7261 (p0) REVERT: A 321 LEU cc_start: 0.9148 (tm) cc_final: 0.8859 (tt) REVERT: A 517 MET cc_start: 0.8782 (mtp) cc_final: 0.8559 (mtp) REVERT: A 885 MET cc_start: 0.8879 (ttp) cc_final: 0.8569 (ttp) REVERT: A 990 ASN cc_start: 0.8902 (p0) cc_final: 0.8591 (p0) REVERT: A 997 GLN cc_start: 0.8834 (tm-30) cc_final: 0.7559 (pm20) REVERT: A 1042 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.5959 (tp) REVERT: A 1165 LEU cc_start: 0.7231 (tp) cc_final: 0.6980 (tp) REVERT: A 1183 PHE cc_start: 0.7365 (p90) cc_final: 0.7009 (p90) REVERT: A 1233 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7011 (m-40) REVERT: A 1320 LEU cc_start: 0.8171 (pt) cc_final: 0.7864 (tt) REVERT: A 1379 MET cc_start: 0.7958 (tpp) cc_final: 0.7499 (tpp) REVERT: B 88 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8372 (t0) REVERT: B 412 ARG cc_start: 0.7405 (mmm160) cc_final: 0.6884 (mmm160) REVERT: B 414 MET cc_start: 0.2175 (tmm) cc_final: 0.1735 (tpt) REVERT: B 464 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8676 (pp) REVERT: B 670 MET cc_start: 0.7492 (tpp) cc_final: 0.6984 (tpt) REVERT: B 944 MET cc_start: 0.7276 (ptm) cc_final: 0.7072 (ptm) REVERT: C 81 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: C 166 ASP cc_start: 0.8489 (m-30) cc_final: 0.8252 (m-30) REVERT: C 327 TYR cc_start: 0.8994 (t80) cc_final: 0.8758 (t80) REVERT: E 57 MET cc_start: 0.6436 (tmm) cc_final: 0.6097 (tpp) REVERT: F 99 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8486 (pt) REVERT: F 130 ILE cc_start: 0.9304 (mm) cc_final: 0.8993 (mm) REVERT: G 41 ASN cc_start: 0.7592 (m110) cc_final: 0.6699 (t0) REVERT: I 15 THR cc_start: 0.7237 (m) cc_final: 0.6676 (p) REVERT: K 112 THR cc_start: 0.8911 (p) cc_final: 0.8525 (t) REVERT: K 126 ASP cc_start: 0.8342 (m-30) cc_final: 0.8084 (m-30) REVERT: N 274 LYS cc_start: 0.5458 (mttm) cc_final: 0.4870 (mmtt) REVERT: N 286 ASP cc_start: 0.7505 (t0) cc_final: 0.7007 (t0) REVERT: N 416 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8004 (pt) REVERT: O 583 TRP cc_start: 0.8625 (t60) cc_final: 0.8079 (t60) REVERT: O 624 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7878 (mm) REVERT: P 14 ASN cc_start: 0.5915 (t0) cc_final: 0.5510 (p0) REVERT: P 49 MET cc_start: 0.7100 (tmm) cc_final: 0.6810 (tmm) REVERT: U 106 ILE cc_start: 0.5741 (OUTLIER) cc_final: 0.5504 (pt) REVERT: U 160 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6768 (mt) REVERT: V 292 LYS cc_start: 0.7381 (mmpt) cc_final: 0.7146 (mttm) REVERT: V 478 GLU cc_start: 0.7550 (pm20) cc_final: 0.6502 (pp20) REVERT: W 316 ARG cc_start: 0.7294 (ptm-80) cc_final: 0.7008 (ptm160) outliers start: 164 outliers final: 79 residues processed: 683 average time/residue: 0.6153 time to fit residues: 710.1659 Evaluate side-chains 565 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 476 time to evaluate : 5.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1233 ASN Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 1032 LEU Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 544 ASN Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 608 ARG Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 297 PHE Chi-restraints excluded: chain P residue 306 ASP Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 450 THR Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 309 HIS Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 433 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 286 optimal weight: 0.2980 chunk 160 optimal weight: 10.0000 chunk 429 optimal weight: 0.1980 chunk 351 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 516 optimal weight: 1.9990 chunk 558 optimal weight: 10.0000 chunk 460 optimal weight: 8.9990 chunk 512 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 414 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 422 ASN A 715 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 GLN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 310 GLN ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 309 HIS W 404 ASN W 506 GLN ** W 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 48467 Z= 0.273 Angle : 0.685 16.741 65892 Z= 0.349 Chirality : 0.045 0.280 7446 Planarity : 0.005 0.063 8071 Dihedral : 15.277 179.651 7415 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 4.11 % Allowed : 14.48 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -3.76 (0.10), residues: 5589 helix: -2.40 (0.10), residues: 1929 sheet: -2.30 (0.20), residues: 600 loop : -2.64 (0.10), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 31 HIS 0.009 0.001 HIS W 309 PHE 0.035 0.002 PHE B 567 TYR 0.026 0.002 TYR E 112 ARG 0.010 0.000 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 516 time to evaluate : 5.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8340 (pt) REVERT: A 219 MET cc_start: 0.7061 (tpp) cc_final: 0.6586 (mtp) REVERT: A 273 MET cc_start: 0.5962 (tpp) cc_final: 0.5532 (mmm) REVERT: A 281 ASN cc_start: 0.7719 (t0) cc_final: 0.7276 (p0) REVERT: A 321 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8836 (tt) REVERT: A 737 LYS cc_start: 0.7468 (ttmm) cc_final: 0.6500 (tptt) REVERT: A 885 MET cc_start: 0.8835 (ttp) cc_final: 0.8606 (ttp) REVERT: A 1042 ILE cc_start: 0.6465 (OUTLIER) cc_final: 0.6030 (tp) REVERT: A 1145 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7957 (mt) REVERT: A 1188 ILE cc_start: 0.7782 (pt) cc_final: 0.7482 (pt) REVERT: A 1320 LEU cc_start: 0.8254 (pt) cc_final: 0.7820 (tt) REVERT: A 1379 MET cc_start: 0.8015 (tpp) cc_final: 0.7514 (tpp) REVERT: B 412 ARG cc_start: 0.7561 (mmm160) cc_final: 0.7277 (mmm160) REVERT: B 464 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8752 (pp) REVERT: B 496 MET cc_start: 0.7983 (mmp) cc_final: 0.7748 (mmp) REVERT: B 670 MET cc_start: 0.7561 (tpp) cc_final: 0.7091 (tpt) REVERT: B 816 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5330 (p0) REVERT: C 81 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: C 166 ASP cc_start: 0.8481 (m-30) cc_final: 0.8205 (m-30) REVERT: C 327 TYR cc_start: 0.9023 (t80) cc_final: 0.8776 (t80) REVERT: E 57 MET cc_start: 0.6531 (tmm) cc_final: 0.6206 (tpp) REVERT: F 99 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8499 (pt) REVERT: F 130 ILE cc_start: 0.9213 (mm) cc_final: 0.8955 (mm) REVERT: G 16 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8295 (p0) REVERT: G 31 ASN cc_start: 0.8524 (m110) cc_final: 0.8175 (m110) REVERT: G 114 MET cc_start: 0.3028 (pmm) cc_final: 0.2648 (pmm) REVERT: I 15 THR cc_start: 0.7384 (m) cc_final: 0.6870 (p) REVERT: K 85 ASP cc_start: 0.8263 (t0) cc_final: 0.8049 (t0) REVERT: K 112 THR cc_start: 0.8924 (p) cc_final: 0.8504 (t) REVERT: K 126 ASP cc_start: 0.8355 (m-30) cc_final: 0.8121 (m-30) REVERT: N 274 LYS cc_start: 0.5654 (mttm) cc_final: 0.5041 (mmtt) REVERT: N 280 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6813 (pp) REVERT: N 286 ASP cc_start: 0.7494 (t0) cc_final: 0.6996 (t0) REVERT: N 416 ILE cc_start: 0.8255 (pp) cc_final: 0.8009 (pt) REVERT: O 197 MET cc_start: 0.7784 (ttp) cc_final: 0.7547 (ttp) REVERT: O 624 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7742 (mt) REVERT: U 106 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5422 (pt) REVERT: U 160 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6613 (mt) REVERT: V 292 LYS cc_start: 0.7592 (mmpt) cc_final: 0.7161 (mttp) REVERT: V 478 GLU cc_start: 0.7568 (pm20) cc_final: 0.6411 (pp20) REVERT: W 316 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.7038 (ptm160) REVERT: W 527 ASP cc_start: 0.4447 (t0) cc_final: 0.4190 (t0) outliers start: 206 outliers final: 117 residues processed: 677 average time/residue: 0.5483 time to fit residues: 626.8668 Evaluate side-chains 593 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 463 time to evaluate : 5.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1302 ASP Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 521 ILE Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 556 ASP Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 608 ARG Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 644 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 297 PHE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain V residue 102 ASP Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 169 HIS Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 450 THR Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 309 HIS Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 450 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 510 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 518 optimal weight: 8.9990 chunk 549 optimal weight: 20.0000 chunk 270 optimal weight: 0.9990 chunk 491 optimal weight: 9.9990 chunk 147 optimal weight: 0.3980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 319 GLN W 404 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 48467 Z= 0.235 Angle : 0.664 15.843 65892 Z= 0.335 Chirality : 0.045 0.274 7446 Planarity : 0.004 0.061 8071 Dihedral : 15.157 178.422 7415 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.37 % Allowed : 16.03 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -3.41 (0.10), residues: 5589 helix: -1.98 (0.11), residues: 1947 sheet: -2.04 (0.21), residues: 567 loop : -2.55 (0.10), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 31 HIS 0.024 0.001 HIS W 309 PHE 0.035 0.002 PHE B 567 TYR 0.018 0.001 TYR B1103 ARG 0.006 0.000 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 500 time to evaluate : 5.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8312 (pt) REVERT: A 123 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7452 (t80) REVERT: A 273 MET cc_start: 0.6015 (tpp) cc_final: 0.5591 (mmm) REVERT: A 281 ASN cc_start: 0.7694 (t0) cc_final: 0.7229 (p0) REVERT: A 321 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8788 (tt) REVERT: A 649 ASP cc_start: 0.7535 (t0) cc_final: 0.7083 (t70) REVERT: A 737 LYS cc_start: 0.7461 (ttmm) cc_final: 0.6732 (tptt) REVERT: A 843 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6595 (tt0) REVERT: A 1042 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6109 (tp) REVERT: A 1145 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7980 (mt) REVERT: A 1320 LEU cc_start: 0.8263 (pt) cc_final: 0.7881 (tt) REVERT: A 1379 MET cc_start: 0.7847 (tpp) cc_final: 0.7344 (tpp) REVERT: B 464 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8771 (pp) REVERT: B 670 MET cc_start: 0.7618 (tpp) cc_final: 0.7061 (tpp) REVERT: B 816 ASP cc_start: 0.5641 (OUTLIER) cc_final: 0.5385 (p0) REVERT: C 81 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: C 166 ASP cc_start: 0.8484 (m-30) cc_final: 0.8205 (m-30) REVERT: E 57 MET cc_start: 0.6589 (tmm) cc_final: 0.6275 (tpp) REVERT: F 99 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8420 (pt) REVERT: F 130 ILE cc_start: 0.9232 (mm) cc_final: 0.8981 (mm) REVERT: G 22 THR cc_start: 0.7356 (m) cc_final: 0.7142 (m) REVERT: G 31 ASN cc_start: 0.8497 (m110) cc_final: 0.8151 (m110) REVERT: I 15 THR cc_start: 0.7386 (m) cc_final: 0.6893 (p) REVERT: K 112 THR cc_start: 0.8980 (p) cc_final: 0.8531 (t) REVERT: K 126 ASP cc_start: 0.8344 (m-30) cc_final: 0.8100 (m-30) REVERT: N 274 LYS cc_start: 0.5676 (mttm) cc_final: 0.5059 (mmtt) REVERT: N 280 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6806 (pp) REVERT: N 286 ASP cc_start: 0.7427 (t0) cc_final: 0.6924 (t0) REVERT: N 416 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.8005 (pt) REVERT: O 603 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5389 (mm) REVERT: O 624 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7851 (mm) REVERT: U 106 ILE cc_start: 0.5757 (OUTLIER) cc_final: 0.5475 (pt) REVERT: U 160 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6611 (mt) REVERT: V 292 LYS cc_start: 0.7607 (mmpt) cc_final: 0.7200 (mttm) REVERT: V 478 GLU cc_start: 0.7602 (pm20) cc_final: 0.6433 (pp20) REVERT: W 316 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.7077 (ptm160) REVERT: W 527 ASP cc_start: 0.4439 (t0) cc_final: 0.3416 (t0) outliers start: 219 outliers final: 140 residues processed: 684 average time/residue: 0.5388 time to fit residues: 629.1439 Evaluate side-chains 624 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 468 time to evaluate : 5.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1079 ARG Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1302 ASP Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 335 LEU Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 521 ILE Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 556 ASP Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 644 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain V residue 16 LEU Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 169 HIS Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 450 THR Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 517 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 457 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 408 optimal weight: 9.9990 chunk 226 optimal weight: 0.0980 chunk 468 optimal weight: 0.8980 chunk 379 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 280 optimal weight: 0.8980 chunk 492 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 715 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 580 ASN ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 309 HIS ** W 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48467 Z= 0.206 Angle : 0.644 14.904 65892 Z= 0.324 Chirality : 0.044 0.281 7446 Planarity : 0.004 0.057 8071 Dihedral : 15.073 178.196 7415 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.45 % Allowed : 16.91 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -3.12 (0.10), residues: 5589 helix: -1.64 (0.11), residues: 1956 sheet: -1.89 (0.22), residues: 553 loop : -2.44 (0.10), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 31 HIS 0.006 0.001 HIS E 99 PHE 0.034 0.001 PHE B 567 TYR 0.024 0.001 TYR U 139 ARG 0.004 0.000 ARG B 788 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 494 time to evaluate : 5.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8303 (pt) REVERT: A 123 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7548 (t80) REVERT: A 273 MET cc_start: 0.5966 (tpp) cc_final: 0.5541 (mmm) REVERT: A 281 ASN cc_start: 0.7672 (t0) cc_final: 0.7300 (p0) REVERT: A 321 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8740 (tt) REVERT: A 649 ASP cc_start: 0.7553 (t0) cc_final: 0.7126 (t70) REVERT: A 737 LYS cc_start: 0.7469 (ttmm) cc_final: 0.6881 (tptt) REVERT: A 843 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6239 (tt0) REVERT: A 1042 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6112 (tp) REVERT: A 1145 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8085 (mt) REVERT: A 1211 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7962 (mmm-85) REVERT: A 1320 LEU cc_start: 0.8231 (pt) cc_final: 0.7870 (tt) REVERT: A 1379 MET cc_start: 0.7859 (tpp) cc_final: 0.7356 (tpp) REVERT: B 198 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: B 305 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8498 (mp) REVERT: B 424 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.9206 (t) REVERT: B 464 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8785 (pp) REVERT: B 670 MET cc_start: 0.7590 (tpp) cc_final: 0.7021 (tpp) REVERT: B 1030 MET cc_start: 0.8436 (mtt) cc_final: 0.8183 (mtt) REVERT: C 81 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: C 166 ASP cc_start: 0.8480 (m-30) cc_final: 0.8200 (m-30) REVERT: C 280 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8785 (mm) REVERT: E 57 MET cc_start: 0.6607 (tmm) cc_final: 0.6326 (tpp) REVERT: F 99 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8359 (pt) REVERT: F 130 ILE cc_start: 0.9201 (mm) cc_final: 0.8954 (mm) REVERT: G 16 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8401 (p0) REVERT: G 31 ASN cc_start: 0.8403 (m110) cc_final: 0.8067 (m110) REVERT: G 80 PHE cc_start: 0.4319 (m-10) cc_final: 0.4054 (m-80) REVERT: I 15 THR cc_start: 0.7393 (m) cc_final: 0.7164 (t) REVERT: K 52 GLN cc_start: 0.8293 (pp30) cc_final: 0.7713 (tp40) REVERT: K 112 THR cc_start: 0.8955 (p) cc_final: 0.8510 (t) REVERT: K 126 ASP cc_start: 0.8326 (m-30) cc_final: 0.8085 (m-30) REVERT: N 274 LYS cc_start: 0.5982 (mttm) cc_final: 0.5223 (mmtt) REVERT: N 280 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6784 (pp) REVERT: N 286 ASP cc_start: 0.7423 (t0) cc_final: 0.6928 (t0) REVERT: N 416 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7960 (pt) REVERT: O 152 HIS cc_start: 0.4592 (OUTLIER) cc_final: 0.4201 (p-80) REVERT: O 603 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5376 (mm) REVERT: P 13 ASP cc_start: 0.7558 (t70) cc_final: 0.7260 (t0) REVERT: U 106 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.5365 (pt) REVERT: U 160 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6603 (mt) REVERT: V 8 HIS cc_start: 0.6848 (m-70) cc_final: 0.6583 (m-70) REVERT: V 255 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8173 (pp) REVERT: V 292 LYS cc_start: 0.7626 (mmpt) cc_final: 0.7196 (mttp) REVERT: V 478 GLU cc_start: 0.7703 (pm20) cc_final: 0.6383 (pp20) REVERT: W 527 ASP cc_start: 0.4424 (t0) cc_final: 0.4121 (t0) outliers start: 223 outliers final: 139 residues processed: 673 average time/residue: 0.5344 time to fit residues: 614.2589 Evaluate side-chains 622 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 462 time to evaluate : 5.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1302 ASP Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 521 ILE Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 608 ARG Chi-restraints excluded: chain O residue 644 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain V residue 16 LEU Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 255 LEU Chi-restraints excluded: chain V residue 445 LEU Chi-restraints excluded: chain V residue 450 THR Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 309 HIS Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 517 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 184 optimal weight: 0.0970 chunk 494 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 549 optimal weight: 20.0000 chunk 456 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 288 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 GLN ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48467 Z= 0.193 Angle : 0.632 14.262 65892 Z= 0.318 Chirality : 0.044 0.279 7446 Planarity : 0.004 0.053 8071 Dihedral : 15.017 178.559 7413 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.51 % Allowed : 17.37 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.91 (0.11), residues: 5589 helix: -1.40 (0.11), residues: 1964 sheet: -1.75 (0.22), residues: 552 loop : -2.38 (0.11), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 31 HIS 0.010 0.001 HIS W 309 PHE 0.033 0.001 PHE B 567 TYR 0.017 0.001 TYR D 65 ARG 0.004 0.000 ARG B 788 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 488 time to evaluate : 5.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8267 (pt) REVERT: A 123 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7526 (t80) REVERT: A 273 MET cc_start: 0.5969 (tpp) cc_final: 0.5550 (mmm) REVERT: A 281 ASN cc_start: 0.7733 (t0) cc_final: 0.7342 (p0) REVERT: A 321 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8719 (tt) REVERT: A 649 ASP cc_start: 0.7573 (t0) cc_final: 0.7157 (t70) REVERT: A 705 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8730 (pt) REVERT: A 737 LYS cc_start: 0.7464 (ttmm) cc_final: 0.6882 (tptt) REVERT: A 843 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6227 (tt0) REVERT: A 1042 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6144 (tp) REVERT: A 1145 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 1301 ARG cc_start: 0.7622 (tpp80) cc_final: 0.7192 (ttm-80) REVERT: A 1379 MET cc_start: 0.7868 (tpp) cc_final: 0.7333 (tpp) REVERT: B 55 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: B 198 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8418 (pm20) REVERT: B 400 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8359 (ttpt) REVERT: B 424 VAL cc_start: 0.9446 (OUTLIER) cc_final: 0.9193 (t) REVERT: B 464 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 670 MET cc_start: 0.7681 (tpp) cc_final: 0.7095 (tpp) REVERT: B 899 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9193 (tt) REVERT: B 1030 MET cc_start: 0.8365 (mtt) cc_final: 0.8121 (mtt) REVERT: B 1117 ILE cc_start: 0.9111 (mm) cc_final: 0.8822 (mt) REVERT: C 81 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: C 166 ASP cc_start: 0.8508 (m-30) cc_final: 0.8241 (m-30) REVERT: E 46 TYR cc_start: 0.6713 (m-10) cc_final: 0.6461 (m-80) REVERT: E 57 MET cc_start: 0.6574 (tmm) cc_final: 0.6272 (tpp) REVERT: F 99 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8378 (pt) REVERT: F 130 ILE cc_start: 0.9193 (mm) cc_final: 0.8942 (mm) REVERT: G 16 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8418 (p0) REVERT: G 31 ASN cc_start: 0.8376 (m110) cc_final: 0.7991 (m110) REVERT: I 15 THR cc_start: 0.7437 (m) cc_final: 0.7202 (t) REVERT: K 52 GLN cc_start: 0.8192 (pp30) cc_final: 0.7625 (tp40) REVERT: K 112 THR cc_start: 0.8978 (p) cc_final: 0.8534 (t) REVERT: K 126 ASP cc_start: 0.8337 (m-30) cc_final: 0.8081 (m-30) REVERT: N 274 LYS cc_start: 0.6031 (mttm) cc_final: 0.5569 (mmtt) REVERT: N 280 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6764 (pp) REVERT: N 286 ASP cc_start: 0.7352 (t0) cc_final: 0.6940 (t0) REVERT: N 416 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7924 (pt) REVERT: O 152 HIS cc_start: 0.4800 (OUTLIER) cc_final: 0.4347 (p-80) REVERT: O 603 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5326 (mm) REVERT: P 13 ASP cc_start: 0.7579 (t70) cc_final: 0.7348 (t0) REVERT: U 106 ILE cc_start: 0.5644 (OUTLIER) cc_final: 0.5110 (pt) REVERT: U 139 TYR cc_start: 0.5210 (m-10) cc_final: 0.4908 (m-80) REVERT: U 160 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6602 (mt) REVERT: V 8 HIS cc_start: 0.6798 (m-70) cc_final: 0.6542 (m-70) REVERT: V 255 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8153 (pp) REVERT: V 292 LYS cc_start: 0.7724 (mmpt) cc_final: 0.7381 (tppt) REVERT: V 452 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.4846 (mt) REVERT: V 478 GLU cc_start: 0.7615 (pm20) cc_final: 0.6503 (pp20) REVERT: W 527 ASP cc_start: 0.4745 (t0) cc_final: 0.4227 (t0) outliers start: 226 outliers final: 160 residues processed: 667 average time/residue: 0.5503 time to fit residues: 624.5281 Evaluate side-chains 649 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 465 time to evaluate : 5.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1302 ASP Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 300 LYS Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 521 ILE Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 644 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain U residue 157 ILE Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain V residue 16 LEU Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 255 LEU Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 445 LEU Chi-restraints excluded: chain V residue 450 THR Chi-restraints excluded: chain V residue 452 LEU Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 309 HIS Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 450 SER Chi-restraints excluded: chain W residue 517 GLU Chi-restraints excluded: chain W residue 522 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 529 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 313 optimal weight: 0.9980 chunk 401 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 chunk 462 optimal weight: 1.9990 chunk 306 optimal weight: 0.4980 chunk 547 optimal weight: 6.9990 chunk 342 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 252 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 HIS ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 523 ASN ** U 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 48467 Z= 0.159 Angle : 0.613 13.823 65892 Z= 0.307 Chirality : 0.043 0.285 7446 Planarity : 0.004 0.050 8071 Dihedral : 14.930 178.655 7413 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.79 % Allowed : 18.27 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.69 (0.11), residues: 5589 helix: -1.14 (0.12), residues: 1946 sheet: -1.66 (0.22), residues: 536 loop : -2.29 (0.11), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP W 435 HIS 0.007 0.001 HIS W 309 PHE 0.030 0.001 PHE B 567 TYR 0.013 0.001 TYR B1103 ARG 0.004 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 509 time to evaluate : 5.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7563 (t80) REVERT: A 273 MET cc_start: 0.5895 (tpp) cc_final: 0.5507 (mmm) REVERT: A 281 ASN cc_start: 0.7685 (t0) cc_final: 0.7317 (p0) REVERT: A 303 LEU cc_start: 0.7769 (pp) cc_final: 0.7285 (mt) REVERT: A 321 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8716 (tt) REVERT: A 649 ASP cc_start: 0.7577 (t0) cc_final: 0.7132 (t70) REVERT: A 705 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8690 (pt) REVERT: A 737 LYS cc_start: 0.7460 (ttmm) cc_final: 0.6888 (tptt) REVERT: A 783 ASN cc_start: 0.6653 (t0) cc_final: 0.5421 (p0) REVERT: A 843 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6182 (tt0) REVERT: A 1042 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.5915 (tp) REVERT: A 1145 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8164 (mt) REVERT: A 1273 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7068 (tmmt) REVERT: A 1301 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7169 (ttm-80) REVERT: A 1379 MET cc_start: 0.7871 (tpp) cc_final: 0.7388 (tpp) REVERT: B 55 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8340 (mtmm) REVERT: B 198 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: B 370 ASP cc_start: 0.8446 (m-30) cc_final: 0.8198 (m-30) REVERT: B 424 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9182 (t) REVERT: B 464 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8748 (tp) REVERT: B 656 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: B 670 MET cc_start: 0.7867 (tpp) cc_final: 0.7331 (ttm) REVERT: B 780 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.6981 (mpt-90) REVERT: B 1030 MET cc_start: 0.8317 (mtt) cc_final: 0.8047 (mtt) REVERT: B 1117 ILE cc_start: 0.9240 (mm) cc_final: 0.8993 (mt) REVERT: C 166 ASP cc_start: 0.8464 (m-30) cc_final: 0.8220 (m-30) REVERT: E 46 TYR cc_start: 0.6689 (m-10) cc_final: 0.6426 (m-80) REVERT: E 57 MET cc_start: 0.6541 (tmm) cc_final: 0.6220 (tpp) REVERT: F 99 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8238 (pt) REVERT: F 130 ILE cc_start: 0.9170 (mm) cc_final: 0.8911 (mm) REVERT: G 31 ASN cc_start: 0.8325 (m110) cc_final: 0.7921 (m110) REVERT: I 15 THR cc_start: 0.7216 (m) cc_final: 0.6743 (p) REVERT: K 52 GLN cc_start: 0.8150 (pp30) cc_final: 0.7568 (tp40) REVERT: K 112 THR cc_start: 0.8973 (p) cc_final: 0.8558 (t) REVERT: K 126 ASP cc_start: 0.8317 (m-30) cc_final: 0.8067 (m-30) REVERT: M 128 GLN cc_start: 0.7788 (tp40) cc_final: 0.7588 (mm-40) REVERT: M 194 LYS cc_start: 0.6642 (tppt) cc_final: 0.5399 (ptpt) REVERT: N 274 LYS cc_start: 0.5843 (mttm) cc_final: 0.5399 (mmtt) REVERT: N 280 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6650 (pp) REVERT: N 286 ASP cc_start: 0.7391 (t0) cc_final: 0.7082 (t0) REVERT: N 416 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7886 (pt) REVERT: O 152 HIS cc_start: 0.5075 (OUTLIER) cc_final: 0.4473 (p-80) REVERT: O 330 LEU cc_start: 0.7067 (mt) cc_final: 0.6754 (mp) REVERT: O 603 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5314 (mm) REVERT: P 19 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.5808 (p-80) REVERT: U 106 ILE cc_start: 0.5609 (OUTLIER) cc_final: 0.5074 (pt) REVERT: U 139 TYR cc_start: 0.5028 (m-10) cc_final: 0.4791 (m-80) REVERT: U 160 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6601 (mt) REVERT: V 8 HIS cc_start: 0.6339 (m-70) cc_final: 0.6099 (m-70) REVERT: V 292 LYS cc_start: 0.7722 (mmpt) cc_final: 0.7388 (tppt) REVERT: V 452 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4672 (mt) REVERT: V 478 GLU cc_start: 0.7861 (pm20) cc_final: 0.6516 (pp20) outliers start: 190 outliers final: 130 residues processed: 666 average time/residue: 0.5377 time to fit residues: 612.8332 Evaluate side-chains 619 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 467 time to evaluate : 5.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1273 LYS Chi-restraints excluded: chain A residue 1302 ASP Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 300 LYS Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 521 ILE Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 644 LEU Chi-restraints excluded: chain P residue 19 HIS Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain V residue 16 LEU Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 445 LEU Chi-restraints excluded: chain V residue 452 LEU Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 309 HIS Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 450 SER Chi-restraints excluded: chain W residue 517 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 338 optimal weight: 0.0980 chunk 218 optimal weight: 0.7980 chunk 326 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 106 optimal weight: 0.3980 chunk 348 optimal weight: 0.7980 chunk 372 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 430 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN D 130 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS P 21 GLN ** U 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 309 HIS W 391 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 48467 Z= 0.152 Angle : 0.622 15.627 65892 Z= 0.307 Chirality : 0.043 0.288 7446 Planarity : 0.003 0.048 8071 Dihedral : 14.859 178.657 7413 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.43 % Allowed : 19.35 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.52 (0.11), residues: 5589 helix: -0.94 (0.12), residues: 1953 sheet: -1.52 (0.22), residues: 549 loop : -2.24 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP W 435 HIS 0.006 0.001 HIS E 99 PHE 0.030 0.001 PHE B 567 TYR 0.015 0.001 TYR A1060 ARG 0.004 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 504 time to evaluate : 5.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7581 (t80) REVERT: A 273 MET cc_start: 0.5851 (tpp) cc_final: 0.5438 (mmm) REVERT: A 281 ASN cc_start: 0.7657 (t0) cc_final: 0.7277 (p0) REVERT: A 303 LEU cc_start: 0.7720 (pp) cc_final: 0.7286 (mt) REVERT: A 321 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8721 (tt) REVERT: A 705 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8561 (pt) REVERT: A 737 LYS cc_start: 0.7447 (ttmm) cc_final: 0.6886 (tptt) REVERT: A 843 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6159 (tt0) REVERT: A 1042 ILE cc_start: 0.6243 (OUTLIER) cc_final: 0.5805 (tp) REVERT: A 1145 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8157 (mt) REVERT: A 1301 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7142 (ttm-80) REVERT: A 1371 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 1379 MET cc_start: 0.7862 (tpp) cc_final: 0.7394 (tpp) REVERT: A 1398 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7172 (p0) REVERT: B 55 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8325 (mtmm) REVERT: B 424 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9176 (t) REVERT: B 656 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: B 670 MET cc_start: 0.7837 (tpp) cc_final: 0.7290 (ttm) REVERT: B 701 TYR cc_start: 0.9086 (m-10) cc_final: 0.8762 (m-80) REVERT: B 1030 MET cc_start: 0.8267 (mtt) cc_final: 0.8000 (mtt) REVERT: B 1117 ILE cc_start: 0.9252 (mm) cc_final: 0.9039 (mt) REVERT: C 166 ASP cc_start: 0.8449 (m-30) cc_final: 0.8231 (m-30) REVERT: E 46 TYR cc_start: 0.6778 (m-10) cc_final: 0.6488 (m-80) REVERT: E 57 MET cc_start: 0.6515 (tmm) cc_final: 0.6213 (tpp) REVERT: E 93 MET cc_start: 0.6109 (pmt) cc_final: 0.5096 (ptm) REVERT: F 99 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8162 (pt) REVERT: F 130 ILE cc_start: 0.9158 (mm) cc_final: 0.8900 (mm) REVERT: G 31 ASN cc_start: 0.8302 (m110) cc_final: 0.7905 (m110) REVERT: G 80 PHE cc_start: 0.3729 (m-80) cc_final: 0.3327 (m-80) REVERT: J 38 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8585 (ttm170) REVERT: K 52 GLN cc_start: 0.8163 (pp30) cc_final: 0.7578 (tp40) REVERT: K 112 THR cc_start: 0.8963 (p) cc_final: 0.8586 (t) REVERT: K 126 ASP cc_start: 0.8301 (m-30) cc_final: 0.8051 (m-30) REVERT: N 274 LYS cc_start: 0.5854 (mttm) cc_final: 0.5404 (mmtt) REVERT: N 280 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6613 (pp) REVERT: N 416 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7885 (pt) REVERT: O 152 HIS cc_start: 0.5080 (OUTLIER) cc_final: 0.4387 (p-80) REVERT: O 208 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6477 (t80) REVERT: O 330 LEU cc_start: 0.7199 (mt) cc_final: 0.6897 (mp) REVERT: O 603 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.5317 (mm) REVERT: P 19 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.5640 (p-80) REVERT: U 106 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.5124 (pt) REVERT: U 160 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6647 (mt) REVERT: V 8 HIS cc_start: 0.6329 (m-70) cc_final: 0.6090 (m-70) REVERT: V 292 LYS cc_start: 0.7730 (mmpt) cc_final: 0.7395 (tppt) REVERT: V 452 LEU cc_start: 0.5113 (OUTLIER) cc_final: 0.4656 (mt) REVERT: V 478 GLU cc_start: 0.7785 (pm20) cc_final: 0.6458 (pp20) outliers start: 172 outliers final: 122 residues processed: 650 average time/residue: 0.5421 time to fit residues: 602.1798 Evaluate side-chains 618 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 474 time to evaluate : 5.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1398 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 300 LYS Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 106 TYR Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 208 TYR Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 521 ILE Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 644 LEU Chi-restraints excluded: chain P residue 19 HIS Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain V residue 16 LEU Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 445 LEU Chi-restraints excluded: chain V residue 452 LEU Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 309 HIS Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 450 SER Chi-restraints excluded: chain W residue 517 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 498 optimal weight: 0.9990 chunk 524 optimal weight: 2.9990 chunk 478 optimal weight: 5.9990 chunk 510 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 400 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 461 optimal weight: 10.0000 chunk 482 optimal weight: 1.9990 chunk 508 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN B 493 GLN B1029 HIS ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 48467 Z= 0.392 Angle : 0.751 13.499 65892 Z= 0.378 Chirality : 0.048 0.270 7446 Planarity : 0.005 0.057 8071 Dihedral : 15.110 179.991 7413 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.91 % Allowed : 19.31 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.71 (0.11), residues: 5589 helix: -1.12 (0.12), residues: 1954 sheet: -1.65 (0.22), residues: 559 loop : -2.35 (0.11), residues: 3076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP W 435 HIS 0.034 0.002 HIS W 309 PHE 0.042 0.002 PHE W 284 TYR 0.027 0.002 TYR B1103 ARG 0.010 0.001 ARG W 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 476 time to evaluate : 6.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7455 (t80) REVERT: A 281 ASN cc_start: 0.7766 (t0) cc_final: 0.7305 (p0) REVERT: A 321 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8745 (tt) REVERT: A 649 ASP cc_start: 0.7703 (t0) cc_final: 0.7255 (t70) REVERT: A 737 LYS cc_start: 0.7463 (ttmm) cc_final: 0.6911 (tptt) REVERT: A 843 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6122 (tt0) REVERT: A 1028 MET cc_start: 0.6016 (mmm) cc_final: 0.5694 (mmt) REVERT: A 1042 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.6110 (tp) REVERT: A 1145 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7953 (mt) REVERT: A 1301 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7278 (ttm-80) REVERT: A 1348 MET cc_start: 0.8053 (pmm) cc_final: 0.7551 (pmm) REVERT: A 1371 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 1379 MET cc_start: 0.8010 (tpp) cc_final: 0.7491 (tpp) REVERT: A 1398 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7090 (p0) REVERT: B 305 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 656 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8332 (m-30) REVERT: B 670 MET cc_start: 0.8086 (tpp) cc_final: 0.7478 (ttm) REVERT: B 701 TYR cc_start: 0.9140 (m-10) cc_final: 0.8845 (m-80) REVERT: B 780 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.7229 (mpt-90) REVERT: B 1030 MET cc_start: 0.8488 (mtt) cc_final: 0.8285 (mtt) REVERT: C 166 ASP cc_start: 0.8397 (m-30) cc_final: 0.8079 (m-30) REVERT: E 57 MET cc_start: 0.6749 (tmm) cc_final: 0.6439 (tpp) REVERT: E 93 MET cc_start: 0.6158 (pmt) cc_final: 0.5185 (ptm) REVERT: F 99 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8654 (pt) REVERT: G 31 ASN cc_start: 0.8315 (m-40) cc_final: 0.7930 (m110) REVERT: G 80 PHE cc_start: 0.4575 (m-80) cc_final: 0.4308 (m-80) REVERT: K 52 GLN cc_start: 0.8261 (pp30) cc_final: 0.7512 (tp40) REVERT: K 112 THR cc_start: 0.9028 (p) cc_final: 0.8672 (t) REVERT: K 126 ASP cc_start: 0.8319 (m-30) cc_final: 0.8086 (m-30) REVERT: N 274 LYS cc_start: 0.5887 (mttm) cc_final: 0.5408 (mmtt) REVERT: N 280 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6611 (pp) REVERT: O 152 HIS cc_start: 0.5337 (OUTLIER) cc_final: 0.4810 (p-80) REVERT: O 208 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6437 (t80) REVERT: O 603 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5501 (mm) REVERT: P 19 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.6063 (p-80) REVERT: U 160 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6843 (mt) REVERT: V 8 HIS cc_start: 0.6905 (m-70) cc_final: 0.6676 (m-70) REVERT: V 292 LYS cc_start: 0.7743 (mmpt) cc_final: 0.7501 (tppt) REVERT: V 452 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4828 (mt) REVERT: V 478 GLU cc_start: 0.7897 (pm20) cc_final: 0.6493 (pp20) outliers start: 196 outliers final: 147 residues processed: 638 average time/residue: 0.5461 time to fit residues: 592.3139 Evaluate side-chains 617 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 452 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1398 ASP Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 300 LYS Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 208 TYR Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 521 ILE Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 644 LEU Chi-restraints excluded: chain P residue 19 HIS Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain V residue 16 LEU Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 169 HIS Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 445 LEU Chi-restraints excluded: chain V residue 452 LEU Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 290 SER Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 450 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 335 optimal weight: 0.7980 chunk 539 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 375 optimal weight: 0.2980 chunk 565 optimal weight: 10.0000 chunk 520 optimal weight: 0.9980 chunk 450 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 348 optimal weight: 6.9990 chunk 276 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 48467 Z= 0.224 Angle : 0.670 14.183 65892 Z= 0.335 Chirality : 0.045 0.279 7446 Planarity : 0.004 0.051 8071 Dihedral : 15.039 179.979 7413 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.43 % Allowed : 20.09 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.58 (0.11), residues: 5589 helix: -0.98 (0.12), residues: 1956 sheet: -1.59 (0.22), residues: 543 loop : -2.29 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP W 435 HIS 0.006 0.001 HIS E 99 PHE 0.037 0.001 PHE W 284 TYR 0.042 0.001 TYR U 139 ARG 0.010 0.000 ARG A1152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11178 Ramachandran restraints generated. 5589 Oldfield, 0 Emsley, 5589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 471 time to evaluate : 5.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7404 (t80) REVERT: A 321 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8743 (tt) REVERT: A 649 ASP cc_start: 0.7657 (t0) cc_final: 0.7220 (t70) REVERT: A 737 LYS cc_start: 0.7457 (ttmm) cc_final: 0.6898 (tptt) REVERT: A 843 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.5965 (tt0) REVERT: A 1042 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6089 (tp) REVERT: A 1145 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8222 (mt) REVERT: A 1273 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7413 (ttpt) REVERT: A 1301 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7184 (ttm-80) REVERT: A 1348 MET cc_start: 0.7976 (pmm) cc_final: 0.7484 (pmm) REVERT: A 1371 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8346 (mm) REVERT: A 1379 MET cc_start: 0.7920 (tpp) cc_final: 0.7423 (tpp) REVERT: A 1398 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7167 (p0) REVERT: B 55 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8425 (mtmm) REVERT: B 198 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: B 305 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8475 (mp) REVERT: B 325 GLU cc_start: 0.6519 (mp0) cc_final: 0.6298 (mp0) REVERT: B 424 VAL cc_start: 0.9416 (OUTLIER) cc_final: 0.9159 (t) REVERT: B 656 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8302 (m-30) REVERT: B 670 MET cc_start: 0.8027 (tpp) cc_final: 0.7283 (ttm) REVERT: B 701 TYR cc_start: 0.9106 (m-10) cc_final: 0.8804 (m-80) REVERT: B 780 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.7107 (mpt-90) REVERT: B 1030 MET cc_start: 0.8376 (mtt) cc_final: 0.8158 (mtt) REVERT: C 38 LYS cc_start: 0.8608 (mttp) cc_final: 0.8382 (mmtt) REVERT: C 166 ASP cc_start: 0.8521 (m-30) cc_final: 0.8262 (m-30) REVERT: E 57 MET cc_start: 0.6666 (tmm) cc_final: 0.6380 (tpp) REVERT: E 93 MET cc_start: 0.6085 (pmt) cc_final: 0.5126 (ptm) REVERT: F 99 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8399 (pt) REVERT: K 52 GLN cc_start: 0.8168 (pp30) cc_final: 0.7427 (tp40) REVERT: K 67 GLU cc_start: 0.7800 (tt0) cc_final: 0.7548 (tt0) REVERT: K 112 THR cc_start: 0.8989 (p) cc_final: 0.8592 (t) REVERT: K 126 ASP cc_start: 0.8307 (m-30) cc_final: 0.8068 (m-30) REVERT: N 274 LYS cc_start: 0.5877 (mttm) cc_final: 0.5403 (mmtt) REVERT: N 280 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6442 (pp) REVERT: N 281 GLU cc_start: 0.6884 (pp20) cc_final: 0.5918 (pm20) REVERT: O 152 HIS cc_start: 0.5313 (OUTLIER) cc_final: 0.4725 (p-80) REVERT: O 208 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6456 (t80) REVERT: O 243 MET cc_start: 0.7839 (mmm) cc_final: 0.7602 (mtt) REVERT: O 603 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5500 (mm) REVERT: P 19 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6052 (p-80) REVERT: U 80 LEU cc_start: 0.6639 (mm) cc_final: 0.6243 (tt) REVERT: U 160 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6641 (mt) REVERT: V 8 HIS cc_start: 0.6524 (m-70) cc_final: 0.6308 (m-70) REVERT: V 255 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8277 (pp) REVERT: V 292 LYS cc_start: 0.7738 (mmpt) cc_final: 0.7406 (tppt) REVERT: V 452 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.4904 (mt) REVERT: V 478 GLU cc_start: 0.7907 (pm20) cc_final: 0.6484 (pp20) outliers start: 172 outliers final: 140 residues processed: 619 average time/residue: 0.5581 time to fit residues: 590.3929 Evaluate side-chains 618 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 455 time to evaluate : 5.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain A residue 1273 LYS Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1398 ASP Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1093 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 ILE Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 300 LYS Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 208 TYR Chi-restraints excluded: chain O residue 213 ASP Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 521 ILE Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 644 LEU Chi-restraints excluded: chain P residue 19 HIS Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 142 ILE Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 ILE Chi-restraints excluded: chain V residue 16 LEU Chi-restraints excluded: chain V residue 134 CYS Chi-restraints excluded: chain V residue 154 VAL Chi-restraints excluded: chain V residue 169 HIS Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 255 LEU Chi-restraints excluded: chain V residue 445 LEU Chi-restraints excluded: chain V residue 452 LEU Chi-restraints excluded: chain V residue 475 LEU Chi-restraints excluded: chain W residue 386 ASN Chi-restraints excluded: chain W residue 450 SER Chi-restraints excluded: chain W residue 522 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 357 optimal weight: 6.9990 chunk 480 optimal weight: 6.9990 chunk 138 optimal weight: 0.0040 chunk 415 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 451 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 463 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.115354 restraints weight = 96587.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.112767 restraints weight = 150730.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111226 restraints weight = 121724.089| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 48467 Z= 0.227 Angle : 0.737 59.200 65892 Z= 0.384 Chirality : 0.045 0.618 7446 Planarity : 0.004 0.051 8071 Dihedral : 15.038 179.977 7413 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.43 % Allowed : 20.23 % Favored : 76.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.42 % 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: -2.57 (0.11), residues: 5589 helix: -0.97 (0.12), residues: 1956 sheet: -1.58 (0.22), residues: 543 loop : -2.28 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP W 435 HIS 0.005 0.001 HIS E 99 PHE 0.034 0.001 PHE W 284 TYR 0.036 0.001 TYR U 139 ARG 0.018 0.000 ARG B 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11088.85 seconds wall clock time: 200 minutes 7.39 seconds (12007.39 seconds total)