Starting phenix.real_space_refine on Sun Feb 25 01:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f41_4181/02_2024/6f41_4181.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f41_4181/02_2024/6f41_4181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f41_4181/02_2024/6f41_4181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f41_4181/02_2024/6f41_4181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f41_4181/02_2024/6f41_4181.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f41_4181/02_2024/6f41_4181.pdb" } resolution = 4.3 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= 0.008 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 132 5.49 5 S 242 5.16 5 C 29871 2.51 5 N 8277 2.21 5 O 9259 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 ARG 528": "NH1" <-> "NH2" Residue "A PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ARG 1068": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" 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 ARG 1054": "NH1" <-> "NH2" Residue "M ARG 93": "NH1" <-> "NH2" Residue "M ARG 95": "NH1" <-> "NH2" 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 106": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 47788 Number of models: 1 Model: "" Number of chains: 29 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: "R" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "X" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1221 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain breaks: 1 Chain: "Y" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1361 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} 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 88.158 76.426 83.592 1.00 99.34 S ATOM 509 SG CYS A 70 90.864 76.952 81.232 1.00 94.11 S ATOM 794 SG CYS A 107 73.192 122.702 95.010 1.00 90.01 S ATOM 817 SG CYS A 110 72.869 123.344 91.506 1.00 94.95 S ATOM 1183 SG CYS A 154 72.458 126.592 94.506 1.00 98.32 S ATOM 1207 SG CYS A 157 69.581 124.871 93.349 1.00103.38 S ATOM 19333 SG CYS B1095 94.227 93.181 73.768 1.00 77.04 S ATOM 19356 SG CYS B1098 90.657 96.284 75.725 1.00 78.95 S ATOM 19422 SG CYS B1107 91.181 91.645 75.645 1.00 75.64 S ATOM 28421 SG CYS I 5 81.105 128.589 160.599 1.00111.12 S ATOM 28440 SG CYS I 8 80.309 125.183 159.841 1.00 88.15 S ATOM 28568 SG CYS I 26 79.312 128.639 157.503 1.00101.32 S ATOM 28591 SG CYS I 29 77.173 126.998 161.287 1.00 67.33 S ATOM 28691 SG CYS J 7 141.078 53.456 128.737 1.00 66.84 S ATOM 28714 SG CYS J 10 144.228 51.842 127.904 1.00 70.27 S ATOM 28994 SG CYS J 45 144.206 55.359 129.638 1.00 84.11 S ATOM 29000 SG CYS J 46 143.537 51.329 131.419 1.00 87.23 S ATOM 30028 SG CYS L 31 98.867 39.710 128.677 1.00 57.85 S ATOM 30152 SG CYS L 48 95.468 38.600 127.878 1.00 63.52 S ATOM 40609 SG CYS V 4 104.770 58.114 78.094 1.00219.38 S ATOM 40632 SG CYS V 7 105.719 54.267 76.853 1.00215.30 S ATOM 40773 SG CYS V 25 106.572 55.716 80.961 1.00191.34 S ATOM 40793 SG CYS V 28 108.277 56.723 77.944 1.00198.77 S Time building chain proxies: 23.99, per 1000 atoms: 0.50 Number of scatterers: 47788 At special positions: 0 Unit cell: (205.2, 174.15, 207.9, 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 132 15.00 O 9259 8.00 N 8277 7.00 C 29871 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: 19.29 Conformation dependent library (CDL) restraints added in 7.9 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 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " 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 I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " 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 29 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " 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 L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 31 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 7 " 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 28 " Number of angles added : 24 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: 211 helices and 58 sheets defined 38.8% alpha, 12.5% beta 39 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 15.60 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.659A pdb=" N ALA A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 removed outlier: 4.064A pdb=" N GLN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 102' Processing helix chain 'A' and resid 116 through 129 removed outlier: 4.406A pdb=" N GLN A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.532A pdb=" N MET A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 206 removed outlier: 4.648A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.618A pdb=" N VAL A 215 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.488A pdb=" N ARG A 252 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 306 removed outlier: 4.511A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.939A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 320 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.257A pdb=" N LYS A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 421 removed outlier: 4.044A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.951A pdb=" N ASN A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) 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 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.913A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.520A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.113A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.936A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.552A pdb=" N LEU A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.582A pdb=" N LEU A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 704 removed outlier: 3.592A pdb=" N ARG A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 722 through 743 removed outlier: 3.638A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 784 removed outlier: 4.014A pdb=" N ILE A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 3.503A pdb=" N MET A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 797 " --> pdb=" O ILE A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 811 removed outlier: 3.781A pdb=" N VAL A 810 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 806 through 811' Processing helix chain 'A' and resid 857 through 874 removed outlier: 4.242A pdb=" N LEU A 862 " --> pdb=" O PRO A 858 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 874 " --> pdb=" O GLU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 889 removed outlier: 3.673A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 889 " --> pdb=" O MET A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 removed outlier: 3.508A pdb=" N ALA A 930 " --> pdb=" O GLU A 927 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 931 " --> pdb=" O GLY A 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 927 through 931' Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.690A pdb=" N ASP A 940 " --> pdb=" O ASN A 936 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.912A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 973 Processing helix chain 'A' and resid 999 through 1026 removed outlier: 3.951A pdb=" N TYR A1005 " --> pdb=" O GLU A1001 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS A1006 " --> pdb=" O ARG A1002 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1008 " --> pdb=" O PHE A1004 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A1009 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A1010 " --> pdb=" O HIS A1006 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.693A pdb=" N GLU A1046 " --> pdb=" O ASP A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 removed outlier: 3.932A pdb=" N LYS A1053 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN A1058 " --> pdb=" O THR A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1081 removed outlier: 3.608A pdb=" N VAL A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A1071 " --> pdb=" O VAL A1067 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1098 removed outlier: 3.847A pdb=" N GLN A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 5.241A pdb=" N GLU A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A1129 " --> pdb=" O ARG A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1162 removed outlier: 3.916A pdb=" N GLY A1159 " --> pdb=" O ARG A1155 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1189 through 1193 removed outlier: 3.682A pdb=" N ILE A1193 " --> pdb=" O LEU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1210 removed outlier: 3.713A pdb=" N ALA A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1260 removed outlier: 4.154A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 4.127A pdb=" N ARG A1265 " --> pdb=" O GLN A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1306 removed outlier: 3.677A pdb=" N CYS A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A1306 " --> pdb=" O ASP A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 4.121A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.618A pdb=" N ILE A1335 " --> pdb=" O ALA A1331 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1339 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A1341 " --> pdb=" O ARG A1337 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 4.206A pdb=" N LEU A1358 " --> pdb=" O HIS A1354 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A1360 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1380 removed outlier: 4.099A pdb=" N LYS A1378 " --> pdb=" O PHE A1374 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A1380 " --> pdb=" O LEU A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1392 through 1395 Processing helix chain 'A' and resid 1396 through 1403 Processing helix chain 'A' and resid 1410 through 1418 removed outlier: 3.504A pdb=" N CYS A1414 " --> pdb=" O GLY A1410 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.894A pdb=" N SER A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1441 removed outlier: 4.013A pdb=" N ASP A1440 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 46 removed outlier: 3.570A pdb=" N HIS B 46 " --> pdb=" O ASP B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.896A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.926A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 71 " --> pdb=" O TYR B 67 " (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 252 through 259 removed outlier: 3.786A pdb=" N VAL B 256 " --> pdb=" O PRO B 252 " (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 287 through 294 removed outlier: 4.047A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 4.268A pdb=" N LEU B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.876A pdb=" N ALA B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 removed outlier: 3.671A pdb=" N TYR B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.826A pdb=" N MET B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 366 removed outlier: 3.822A pdb=" N ILE B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 366' 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 380 through 407 removed outlier: 4.935A pdb=" N LEU B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 400 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 removed outlier: 3.708A pdb=" N SER B 421 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 439 removed outlier: 4.289A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.798A pdb=" N MET B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 536 removed outlier: 3.715A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.679A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 581 " --> pdb=" O HIS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 633 removed outlier: 3.580A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 652 through 657 removed outlier: 4.052A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.860A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 4.276A pdb=" N THR B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 931 removed outlier: 3.691A pdb=" N ASP B 930 " --> pdb=" O LYS B 927 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 931 " --> pdb=" O GLN B 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 931' Processing helix chain 'B' and resid 948 through 953 Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.956A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 966 " --> pdb=" O ILE B 962 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 968 " --> pdb=" O GLY B 964 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 993 removed outlier: 4.262A pdb=" N ILE B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1072 removed outlier: 3.670A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B1072 " --> pdb=" O ASP B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1082 Processing helix chain 'B' and resid 1123 through 1127 Processing helix chain 'B' and resid 1127 through 1135 removed outlier: 4.530A pdb=" N LEU B1133 " --> pdb=" O PHE B1129 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.804A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET C 71 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.842A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (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 241 through 249 removed outlier: 3.927A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 309 through 327 removed outlier: 3.542A pdb=" N ILE C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 removed outlier: 3.626A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 72 removed outlier: 3.671A pdb=" N ILE D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 removed outlier: 3.694A pdb=" N GLU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.656A pdb=" N LEU D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 161 removed outlier: 3.583A pdb=" N LEU D 154 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 27 removed outlier: 3.974A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 35 removed outlier: 3.504A pdb=" N GLU E 34 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 35 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 35' Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.784A pdb=" N PHE E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR E 46 " --> pdb=" O PHE E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.639A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE E 100 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 4.065A pdb=" N MET E 121 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 157 through 165 removed outlier: 3.536A pdb=" N LYS E 161 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 88 through 103 removed outlier: 3.659A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 125 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.605A pdb=" N ASN G 32 " --> pdb=" O HIS G 28 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS G 33 " --> pdb=" O GLN G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 211 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: 3.849A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.923A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 52 removed outlier: 4.164A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.589A 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: 3.881A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.309A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 124 removed outlier: 3.748A pdb=" N LEU K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 142 removed outlier: 3.712A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 131 removed outlier: 3.548A pdb=" N TYR M 131 " --> pdb=" O GLN M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 removed outlier: 3.519A pdb=" N ALA M 136 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 201 removed outlier: 3.900A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN M 190 " --> pdb=" O ILE M 186 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN M 195 " --> pdb=" O VAL M 191 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 236 removed outlier: 3.577A pdb=" N ALA M 233 " --> pdb=" O GLY M 229 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS M 234 " --> pdb=" O SER M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 261 removed outlier: 3.794A pdb=" N LYS M 261 " --> pdb=" O ASP M 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 297 removed outlier: 4.029A pdb=" N LEU N 280 " --> pdb=" O ALA N 276 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU N 281 " --> pdb=" O ALA N 277 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU N 282 " --> pdb=" O ALA N 278 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN N 288 " --> pdb=" O ASN N 284 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE N 290 " --> pdb=" O ASP N 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS N 293 " --> pdb=" O HIS N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 300 No H-bonds generated for 'chain 'N' and resid 298 through 300' Processing helix chain 'O' and resid 45 through 56 removed outlier: 4.093A pdb=" N GLU O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.130A 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: 3.749A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 100 removed outlier: 3.634A pdb=" N GLN O 100 " --> pdb=" O VAL O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 130 removed outlier: 4.185A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 4.211A pdb=" N ILE O 137 " --> pdb=" O SER O 133 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP O 138 " --> pdb=" O GLY O 134 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU O 139 " --> pdb=" O LEU O 135 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE O 140 " --> pdb=" O ILE O 136 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE O 141 " --> pdb=" O ILE O 137 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 164 removed outlier: 3.741A pdb=" N ALA O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE O 164 " --> pdb=" O VAL O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 176 removed outlier: 3.925A pdb=" N LEU O 175 " --> pdb=" O VAL O 171 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 171 through 176' Processing helix chain 'O' and resid 183 through 196 removed outlier: 3.807A pdb=" N PHE O 191 " --> pdb=" O ILE O 187 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.705A pdb=" N PHE O 217 " --> pdb=" O ASP O 213 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 218 through 224 removed outlier: 3.683A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 258 removed outlier: 4.234A pdb=" N ALA O 241 " --> pdb=" O LYS O 237 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 259 through 262 removed outlier: 3.735A pdb=" N ILE O 262 " --> pdb=" O LEU O 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 259 through 262' Processing helix chain 'O' and resid 283 through 304 removed outlier: 4.230A pdb=" N PHE O 287 " --> pdb=" O ASN O 283 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE O 297 " --> pdb=" O SER O 293 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN O 298 " --> pdb=" O LYS O 294 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU O 299 " --> pdb=" O GLN O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 319 removed outlier: 3.712A pdb=" N ALA O 309 " --> pdb=" O GLY O 305 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN O 310 " --> pdb=" O SER O 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA O 315 " --> pdb=" O VAL O 311 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU O 316 " --> pdb=" O TYR O 312 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR O 319 " --> pdb=" O ALA O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 333 removed outlier: 4.060A pdb=" N THR O 333 " --> pdb=" O PRO O 329 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 343 Processing helix chain 'O' and resid 343 through 355 removed outlier: 3.873A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA O 349 " --> pdb=" O PHE O 345 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS O 355 " --> pdb=" O LEU O 351 " (cutoff:3.500A) Processing helix chain 'O' and resid 365 through 370 removed outlier: 4.041A pdb=" N HIS O 369 " --> pdb=" O ASP O 365 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU O 370 " --> pdb=" O LEU O 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 365 through 370' Processing helix chain 'O' and resid 451 through 463 removed outlier: 3.762A pdb=" N LEU O 457 " --> pdb=" O ILE O 453 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE O 459 " --> pdb=" O SER O 455 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU O 460 " --> pdb=" O HIS O 456 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA O 461 " --> pdb=" O LEU O 457 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER O 462 " --> pdb=" O LYS O 458 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 500 removed outlier: 3.594A pdb=" N TYR O 492 " --> pdb=" O LYS O 488 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU O 493 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL O 495 " --> pdb=" O VAL O 491 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE O 496 " --> pdb=" O TYR O 492 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.789A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP O 513 " --> pdb=" O ARG O 509 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 521 through 526 Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.934A pdb=" N ILE O 533 " --> pdb=" O LYS O 529 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG O 534 " --> pdb=" O GLU O 530 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER O 535 " --> pdb=" O LYS O 531 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR O 536 " --> pdb=" O ASP O 532 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA O 538 " --> pdb=" O ARG O 534 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER O 539 " --> pdb=" O SER O 535 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU O 540 " --> pdb=" O THR O 536 " (cutoff:3.500A) Processing helix chain 'O' and resid 554 through 558 removed outlier: 4.406A pdb=" N ARG O 557 " --> pdb=" O THR O 554 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER O 558 " --> pdb=" O ALA O 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 554 through 558' Processing helix chain 'O' and resid 571 through 589 removed outlier: 3.678A pdb=" N ASN O 575 " --> pdb=" O THR O 571 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET O 577 " --> pdb=" O SER O 573 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN O 579 " --> pdb=" O ASN O 575 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN O 584 " --> pdb=" O ASN O 580 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU O 588 " --> pdb=" O ASN O 584 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU O 589 " --> pdb=" O MET O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 589 through 598 removed outlier: 3.661A pdb=" N GLU O 593 " --> pdb=" O LEU O 589 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU O 598 " --> pdb=" O LYS O 594 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 removed outlier: 3.963A pdb=" N LEU O 603 " --> pdb=" O ASN O 599 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS O 604 " --> pdb=" O SER O 600 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS O 605 " --> pdb=" O THR O 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 624 through 629 Processing helix chain 'O' and resid 631 through 650 removed outlier: 3.508A pdb=" N VAL O 637 " --> pdb=" O ARG O 633 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA O 639 " --> pdb=" O LEU O 635 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU O 644 " --> pdb=" O ARG O 640 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU O 647 " --> pdb=" O ARG O 643 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) Processing helix chain 'O' and resid 651 through 653 No H-bonds generated for 'chain 'O' and resid 651 through 653' Processing helix chain 'P' and resid 12 through 23 removed outlier: 3.504A pdb=" N LEU P 18 " --> pdb=" O ASN P 14 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS P 19 " --> pdb=" O ALA P 15 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 40 removed outlier: 4.266A pdb=" N LYS P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 58 removed outlier: 3.967A pdb=" N SER P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 85 removed outlier: 3.732A pdb=" N ALA P 80 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS P 82 " --> pdb=" O SER P 78 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR P 85 " --> pdb=" O GLN P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 101 removed outlier: 3.864A pdb=" N TYR P 96 " --> pdb=" O LEU P 92 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE P 97 " --> pdb=" O VAL P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 117 through 131 removed outlier: 3.765A pdb=" N SER P 127 " --> pdb=" O LYS P 123 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER P 130 " --> pdb=" O LYS P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 188 removed outlier: 4.239A pdb=" N LEU P 178 " --> pdb=" O PHE P 174 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP P 183 " --> pdb=" O LEU P 179 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG P 184 " --> pdb=" O THR P 180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE P 186 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU P 188 " --> pdb=" O ARG P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 223 removed outlier: 4.194A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 219 through 223' Processing helix chain 'P' and resid 236 through 250 removed outlier: 3.554A pdb=" N GLU P 245 " --> pdb=" O ARG P 241 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL P 246 " --> pdb=" O SER P 242 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU P 247 " --> pdb=" O LEU P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 271 Processing helix chain 'Q' and resid 55 through 67 removed outlier: 4.104A pdb=" N ILE Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN Q 60 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE Q 61 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 87 removed outlier: 3.693A pdb=" N VAL U 85 " --> pdb=" O ASP U 81 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA U 86 " --> pdb=" O LEU U 82 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU U 87 " --> pdb=" O LYS U 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 81 through 87' Processing helix chain 'U' and resid 128 through 143 removed outlier: 3.769A pdb=" N ALA U 135 " --> pdb=" O ASP U 131 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG U 137 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA U 140 " --> pdb=" O SER U 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE U 142 " --> pdb=" O LYS U 138 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE U 143 " --> pdb=" O TYR U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 179 Processing helix chain 'U' and resid 221 through 230 removed outlier: 4.093A pdb=" N GLN U 225 " --> pdb=" O GLU U 221 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA U 226 " --> pdb=" O GLU U 222 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA U 229 " --> pdb=" O GLN U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 235 Processing helix chain 'V' and resid 74 through 94 removed outlier: 3.734A pdb=" N LEU V 80 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR V 92 " --> pdb=" O ARG V 88 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 114 removed outlier: 4.191A pdb=" N THR V 101 " --> pdb=" O PRO V 97 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA V 103 " --> pdb=" O TYR V 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN V 106 " --> pdb=" O ASP V 102 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA V 113 " --> pdb=" O LYS V 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 137 removed outlier: 3.582A pdb=" N ILE V 126 " --> pdb=" O SER V 122 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA V 127 " --> pdb=" O GLN V 123 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA V 133 " --> pdb=" O CYS V 129 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU V 137 " --> pdb=" O ALA V 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 150 removed outlier: 3.525A pdb=" N SER V 147 " --> pdb=" O LEU V 143 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG V 149 " --> pdb=" O ASP V 145 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU V 150 " --> pdb=" O PHE V 146 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 166 removed outlier: 3.802A pdb=" N ILE V 157 " --> pdb=" O SER V 153 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR V 160 " --> pdb=" O SER V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 177 through 179 No H-bonds generated for 'chain 'V' and resid 177 through 179' Processing helix chain 'V' and resid 180 through 186 removed outlier: 4.087A pdb=" N HIS V 184 " --> pdb=" O LEU V 180 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA V 186 " --> pdb=" O ILE V 182 " (cutoff:3.500A) Processing helix chain 'V' and resid 196 through 212 removed outlier: 3.618A pdb=" N ASP V 201 " --> pdb=" O LYS V 197 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA V 202 " --> pdb=" O VAL V 198 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS V 211 " --> pdb=" O GLN V 207 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP V 212 " --> pdb=" O ARG V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 219 through 234 removed outlier: 4.060A pdb=" N ILE V 228 " --> pdb=" O ALA V 224 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU V 229 " --> pdb=" O GLY V 225 " (cutoff:3.500A) Processing helix chain 'V' and resid 242 through 249 Processing helix chain 'V' and resid 252 through 264 removed outlier: 3.771A pdb=" N GLN V 257 " --> pdb=" O GLU V 253 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG V 258 " --> pdb=" O THR V 254 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU V 259 " --> pdb=" O LEU V 255 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN V 264 " --> pdb=" O ASN V 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 267 through 271 Processing helix chain 'V' and resid 287 through 297 removed outlier: 3.795A pdb=" N VAL V 291 " --> pdb=" O PRO V 287 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN V 293 " --> pdb=" O SER V 289 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU V 297 " --> pdb=" O ASN V 293 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 453 Processing helix chain 'V' and resid 479 through 491 removed outlier: 3.609A pdb=" N ARG V 485 " --> pdb=" O LYS V 481 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE V 486 " --> pdb=" O LEU V 482 " (cutoff:3.500A) Processing helix chain 'V' and resid 492 through 507 removed outlier: 3.534A pdb=" N LEU V 496 " --> pdb=" O ALA V 492 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU V 499 " --> pdb=" O LEU V 495 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN V 505 " --> pdb=" O LYS V 501 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 319 removed outlier: 3.674A pdb=" N ALA W 299 " --> pdb=" O LYS W 295 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS W 300 " --> pdb=" O SER W 296 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU W 305 " --> pdb=" O LYS W 301 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG W 308 " --> pdb=" O LEU W 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS W 309 " --> pdb=" O GLU W 305 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU W 312 " --> pdb=" O ARG W 308 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU W 313 " --> pdb=" O HIS W 309 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG W 314 " --> pdb=" O LEU W 310 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN W 319 " --> pdb=" O MET W 315 " (cutoff:3.500A) Processing helix chain 'W' and resid 384 through 393 removed outlier: 4.105A pdb=" N GLU W 390 " --> pdb=" O ASN W 386 " (cutoff:3.500A) Processing helix chain 'W' and resid 421 through 435 removed outlier: 3.680A pdb=" N ILE W 426 " --> pdb=" O VAL W 422 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS W 427 " --> pdb=" O GLU W 423 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS W 430 " --> pdb=" O ILE W 426 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA W 431 " --> pdb=" O LYS W 427 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP W 435 " --> pdb=" O ALA W 431 " (cutoff:3.500A) Processing helix chain 'W' and resid 440 through 446 removed outlier: 4.444A pdb=" N GLN W 444 " --> pdb=" O ASN W 440 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU W 445 " --> pdb=" O LEU W 441 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR W 446 " --> pdb=" O ILE W 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 440 through 446' Processing helix chain 'W' and resid 450 through 465 removed outlier: 3.652A pdb=" N VAL W 454 " --> pdb=" O SER W 450 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS W 455 " --> pdb=" O ARG W 451 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU W 461 " --> pdb=" O LYS W 457 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU W 462 " --> pdb=" O PHE W 458 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS W 463 " --> pdb=" O VAL W 459 " (cutoff:3.500A) Processing helix chain 'W' and resid 465 through 470 removed outlier: 3.658A pdb=" N ILE W 469 " --> pdb=" O ARG W 465 " (cutoff:3.500A) Processing helix chain 'W' and resid 482 through 490 removed outlier: 4.623A pdb=" N CYS W 486 " --> pdb=" O ASP W 482 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS W 490 " --> pdb=" O CYS W 486 " (cutoff:3.500A) Processing helix chain 'W' and resid 497 through 537 removed outlier: 3.810A pdb=" N LEU W 502 " --> pdb=" O PHE W 498 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE W 503 " --> pdb=" O ASN W 499 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU W 505 " --> pdb=" O LYS W 501 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU W 526 " --> pdb=" O THR W 522 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU W 533 " --> pdb=" O THR W 529 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 1405 through 1407 removed outlier: 3.538A pdb=" N GLU A 17 " --> pdb=" O ARG B1140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.782A pdb=" N VAL A 32 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.501A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.561A pdb=" N HIS B1036 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 376 " --> pdb=" O ARG B1038 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 377 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN A 518 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 475 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 500 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.590A pdb=" N ARG A 464 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 628 removed outlier: 3.888A pdb=" N ALA A 628 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 814 through 815 removed outlier: 3.923A pdb=" N GLY A 814 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 removed outlier: 3.610A pdb=" N ARG A 905 " --> pdb=" O SER A 897 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1281 through 1282 removed outlier: 3.934A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 4.113A pdb=" N LYS A1273 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1174 through 1176 removed outlier: 4.013A pdb=" N VAL A1176 " --> pdb=" O PHE A1183 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE A1183 " --> pdb=" O VAL A1176 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A1229 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A1231 " --> pdb=" O ASN A1223 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A1223 " --> pdb=" O ALA A1231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 142 through 147 removed outlier: 3.768A pdb=" N SER F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG F 135 " --> pdb=" O LYS A1429 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A1429 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.574A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 93 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR B 136 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B 132 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 127 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY B 150 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE B 129 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU B 148 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL B 131 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL W 397 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 377 removed outlier: 3.677A pdb=" N GLN B 199 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 474 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 198 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 512 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 218 through 221 Processing sheet with id=AC2, first strand: chain 'B' and resid 235 through 236 Processing sheet with id=AC3, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC4, first strand: chain 'B' and resid 560 through 561 removed outlier: 6.077A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 724 through 728 removed outlier: 4.003A pdb=" N CYS B 785 " --> pdb=" O ARG B 904 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 904 " --> pdb=" O CYS B 785 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 724 through 728 removed outlier: 4.003A pdb=" N CYS B 785 " --> pdb=" O ARG B 904 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 904 " --> pdb=" O CYS B 785 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC8, first strand: chain 'B' and resid 753 through 759 removed outlier: 4.464A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 911 through 912 removed outlier: 7.405A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 839 through 843 removed outlier: 5.878A pdb=" N GLN B 840 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR B 873 " --> pdb=" O GLN B 840 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 842 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL B 871 " --> pdb=" O TYR B 842 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AD3, first strand: chain 'B' and resid 1043 through 1044 removed outlier: 6.455A pdb=" N ARG B1043 " --> pdb=" O VAL V 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id=AD5, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.610A pdb=" N PHE C 54 " --> pdb=" O PHE C 300 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 4 through 5 removed outlier: 4.189A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.942A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 11.208A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.630A pdb=" N ILE C 132 " --> pdb=" O CYS C 208 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS C 208 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 134 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 136 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 204 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.724A pdb=" N VAL C 162 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 256 through 258 removed outlier: 3.536A pdb=" N TYR C 266 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.851A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 74 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.851A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 74 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR G 53 " --> pdb=" O THR G 71 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.648A pdb=" N PHE E 60 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL E 80 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 153 through 155 removed outlier: 3.818A pdb=" N GLU E 194 " --> pdb=" O CYS E 214 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 85 through 87 Processing sheet with id=AE6, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.938A pdb=" N ALA G 195 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 95 through 96 removed outlier: 3.530A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 57 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE H 6 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 28 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP H 41 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H 105 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR H 115 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AE9, first strand: chain 'K' and resid 60 through 66 removed outlier: 3.643A pdb=" N ALA K 61 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE K 105 " --> pdb=" O ALA K 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE K 103 " --> pdb=" O PHE K 63 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 118 through 123 removed outlier: 3.971A pdb=" N VAL M 151 " --> pdb=" O GLN M 178 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN M 178 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL M 87 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU M 179 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN M 89 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL N 394 " --> pdb=" O VAL N 412 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY N 410 " --> pdb=" O ALA N 396 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER N 398 " --> pdb=" O LEU N 408 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU N 408 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N PHE N 304 " --> pdb=" O ASP N 413 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS N 415 " --> pdb=" O PHE N 304 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL N 306 " --> pdb=" O LYS N 415 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL N 417 " --> pdb=" O VAL N 306 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN N 308 " --> pdb=" O VAL N 417 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR N 419 " --> pdb=" O GLN N 308 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N VAL M 168 " --> pdb=" O GLU M 73 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N LEU M 170 " --> pdb=" O PRO M 75 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER N 372 " --> pdb=" O ARG N 364 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 247 through 248 Processing sheet with id=AF3, first strand: chain 'M' and resid 96 through 97 removed outlier: 3.689A pdb=" N LYS M 100 " --> pdb=" O VAL M 97 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 218 through 219 removed outlier: 6.624A pdb=" N SER M 218 " --> pdb=" O VAL W 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'O' and resid 104 through 110 removed outlier: 3.661A pdb=" N LYS O 105 " --> pdb=" O TYR O 121 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 169 through 170 Processing sheet with id=AF7, first strand: chain 'O' and resid 549 through 552 removed outlier: 3.532A pdb=" N VAL O 551 " --> pdb=" O VAL O 563 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL O 563 " --> pdb=" O VAL O 551 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 61 through 62 Processing sheet with id=AF9, first strand: chain 'P' and resid 135 through 137 removed outlier: 4.276A pdb=" N ILE P 147 " --> pdb=" O VAL P 137 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 253 through 256 Processing sheet with id=AG2, first strand: chain 'U' and resid 66 through 70 removed outlier: 5.309A pdb=" N LEU U 67 " --> pdb=" O SER U 163 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER U 163 " --> pdb=" O LEU U 67 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN U 69 " --> pdb=" O VAL U 161 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE U 160 " --> pdb=" O GLY U 216 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY U 216 " --> pdb=" O ILE U 160 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU U 205 " --> pdb=" O VAL U 213 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR U 215 " --> pdb=" O VAL U 203 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL U 203 " --> pdb=" O THR U 215 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 72 through 74 removed outlier: 3.664A pdb=" N MET U 121 " --> pdb=" O VAL U 74 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 364 through 365 1244 hydrogen bonds defined for protein. 3498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 23.72 Time building geometry restraints manager: 20.34 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: 15116 1.34 - 1.46: 7785 1.46 - 1.58: 25353 1.58 - 1.70: 259 1.70 - 1.82: 392 Bond restraints: 48905 Sorted by residual: bond pdb=" CB ASN O 229 " pdb=" CG ASN O 229 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.48e+00 bond pdb=" C3' DA X 28 " pdb=" O3' DA X 28 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.40e+00 bond pdb=" C3' DA Y 61 " pdb=" O3' DA Y 61 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CA ASN B 814 " pdb=" CB ASN B 814 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.26e+00 bond pdb=" CA ASP A 721 " pdb=" CB ASP A 721 " ideal model delta sigma weight residual 1.530 1.549 -0.018 1.69e-02 3.50e+03 1.18e+00 ... (remaining 48900 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.65: 1615 105.65 - 112.74: 25924 112.74 - 119.83: 16462 119.83 - 126.93: 21784 126.93 - 134.02: 782 Bond angle restraints: 66567 Sorted by residual: angle pdb=" N ILE O 364 " pdb=" CA ILE O 364 " pdb=" C ILE O 364 " ideal model delta sigma weight residual 113.71 107.65 6.06 9.50e-01 1.11e+00 4.07e+01 angle pdb=" C ALA A 720 " pdb=" N ASP A 721 " pdb=" CA ASP A 721 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.01e+01 angle pdb=" CA LEU A1039 " pdb=" CB LEU A1039 " pdb=" CG LEU A1039 " ideal model delta sigma weight residual 116.30 131.66 -15.36 3.50e+00 8.16e-02 1.93e+01 angle pdb=" C CYS A 70 " pdb=" N HIS A 71 " pdb=" CA HIS A 71 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 angle pdb=" N GLY W 287 " pdb=" CA GLY W 287 " pdb=" C GLY W 287 " ideal model delta sigma weight residual 113.18 122.43 -9.25 2.37e+00 1.78e-01 1.52e+01 ... (remaining 66562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 28856 35.96 - 71.92: 862 71.92 - 107.89: 32 107.89 - 143.85: 1 143.85 - 179.81: 2 Dihedral angle restraints: 29753 sinusoidal: 13198 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 180.00 140.66 39.34 0 5.00e+00 4.00e-02 6.19e+01 dihedral pdb=" CA ASP C 273 " pdb=" C ASP C 273 " pdb=" N THR C 274 " pdb=" CA THR C 274 " ideal model delta harmonic sigma weight residual 180.00 147.52 32.48 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA ILE U 70 " pdb=" C ILE U 70 " pdb=" N VAL U 71 " pdb=" CA VAL U 71 " ideal model delta harmonic sigma weight residual 180.00 147.64 32.36 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 29750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 5867 0.047 - 0.094: 1345 0.094 - 0.141: 288 0.141 - 0.188: 25 0.188 - 0.236: 3 Chirality restraints: 7528 Sorted by residual: chirality pdb=" CG LEU A1039 " pdb=" CB LEU A1039 " pdb=" CD1 LEU A1039 " pdb=" CD2 LEU A1039 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 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 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE O 521 " pdb=" CA ILE O 521 " pdb=" CG1 ILE O 521 " pdb=" CG2 ILE O 521 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 7525 not shown) Planarity restraints: 8090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1351 " 0.059 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO A1352 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A1352 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1352 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 123 " -0.049 5.00e-02 4.00e+02 7.49e-02 8.97e+00 pdb=" N PRO M 124 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO M 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO M 124 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 832 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO A 833 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 833 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 833 " -0.038 5.00e-02 4.00e+02 ... (remaining 8087 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3443 2.74 - 3.28: 48518 3.28 - 3.82: 76159 3.82 - 4.36: 90146 4.36 - 4.90: 144286 Nonbonded interactions: 362552 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" O SER A1349 " model vdw 2.195 2.440 nonbonded pdb=" N CYS A 70 " pdb="ZN ZN A1501 " model vdw 2.208 2.310 nonbonded pdb=" OD1 ASN B 774 " pdb=" OG SER B 777 " model vdw 2.209 2.440 nonbonded pdb=" O PHE V 146 " pdb=" NH1 ARG V 149 " model vdw 2.214 2.520 nonbonded pdb=" ND2 ASN W 407 " pdb=" OP1 DG Y 65 " model vdw 2.221 2.520 ... (remaining 362547 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 5.670 Check model and map are aligned: 0.630 Set scattering table: 0.410 Process input model: 140.930 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.150 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 0.036 48905 Z= 0.127 Angle : 0.639 15.361 66567 Z= 0.350 Chirality : 0.042 0.236 7528 Planarity : 0.006 0.090 8090 Dihedral : 15.368 179.808 19017 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.88 % Favored : 90.07 % Rotamer: Outliers : 0.80 % Allowed : 10.42 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.06 % 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: -4.92 (0.08), residues: 5589 helix: -4.07 (0.06), residues: 1731 sheet: -2.64 (0.18), residues: 621 loop : -3.01 (0.09), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 106 HIS 0.010 0.001 HIS A 71 PHE 0.025 0.001 PHE B1018 TYR 0.024 0.001 TYR E 112 ARG 0.015 0.001 ARG U 107 *********************** 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 1150 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1110 time to evaluate : 5.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8358 (m-80) cc_final: 0.8155 (m-80) REVERT: A 134 ASN cc_start: 0.8002 (t0) cc_final: 0.6123 (t0) REVERT: A 138 MET cc_start: 0.8173 (ptp) cc_final: 0.7473 (ptp) REVERT: A 142 LYS cc_start: 0.9162 (tppp) cc_final: 0.8775 (mmmt) REVERT: A 273 MET cc_start: 0.5270 (mtp) cc_final: 0.5002 (ttp) REVERT: A 320 GLN cc_start: 0.8857 (tt0) cc_final: 0.8578 (tp40) REVERT: A 390 ASP cc_start: 0.8274 (p0) cc_final: 0.8056 (p0) REVERT: A 545 LYS cc_start: 0.9255 (ttpt) cc_final: 0.8789 (ttmt) REVERT: A 572 ASP cc_start: 0.8750 (p0) cc_final: 0.8472 (p0) REVERT: A 582 MET cc_start: 0.8698 (mtm) cc_final: 0.8454 (mtm) REVERT: A 701 CYS cc_start: 0.8762 (m) cc_final: 0.8466 (t) REVERT: A 745 PHE cc_start: 0.7535 (p90) cc_final: 0.6681 (m-10) REVERT: A 922 ASP cc_start: 0.7563 (m-30) cc_final: 0.6727 (m-30) REVERT: A 929 ASN cc_start: 0.8067 (m-40) cc_final: 0.7603 (t0) REVERT: A 985 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8118 (ttpt) REVERT: A 1343 MET cc_start: 0.8761 (mmt) cc_final: 0.8188 (mmm) REVERT: B 53 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8092 (mmtp) REVERT: B 122 ASP cc_start: 0.8622 (m-30) cc_final: 0.8290 (m-30) REVERT: B 256 VAL cc_start: 0.9328 (m) cc_final: 0.8701 (p) REVERT: B 368 ASP cc_start: 0.8790 (p0) cc_final: 0.8586 (p0) REVERT: B 445 LYS cc_start: 0.8542 (tttp) cc_final: 0.8076 (tppt) REVERT: B 520 ILE cc_start: 0.9726 (mt) cc_final: 0.9341 (mt) REVERT: B 591 TYR cc_start: 0.7262 (t80) cc_final: 0.6943 (t80) REVERT: B 773 LEU cc_start: 0.8905 (pt) cc_final: 0.8459 (pp) REVERT: B 809 MET cc_start: 0.7769 (mtm) cc_final: 0.7568 (mtt) REVERT: B 931 MET cc_start: 0.8629 (mpp) cc_final: 0.7937 (mpp) REVERT: B 953 MET cc_start: 0.8602 (mtt) cc_final: 0.8174 (mtm) REVERT: B 1049 GLN cc_start: 0.9002 (mp10) cc_final: 0.8410 (mp10) REVERT: B 1081 GLU cc_start: 0.8254 (pp20) cc_final: 0.7994 (pp20) REVERT: B 1119 MET cc_start: 0.8201 (mtm) cc_final: 0.7876 (mtp) REVERT: C 32 ASN cc_start: 0.8434 (t0) cc_final: 0.7923 (t0) REVERT: C 115 TRP cc_start: 0.8797 (m100) cc_final: 0.8536 (m-90) REVERT: C 317 SER cc_start: 0.9591 (t) cc_final: 0.9350 (p) REVERT: E 99 HIS cc_start: 0.8218 (m-70) cc_final: 0.7899 (m170) REVERT: E 179 GLN cc_start: 0.8301 (pt0) cc_final: 0.8030 (pt0) REVERT: E 214 CYS cc_start: 0.8353 (t) cc_final: 0.6368 (p) REVERT: E 215 MET cc_start: 0.7212 (pp-130) cc_final: 0.6814 (ppp) REVERT: G 36 ASN cc_start: 0.7101 (t0) cc_final: 0.6883 (t0) REVERT: G 92 CYS cc_start: 0.5702 (m) cc_final: 0.5434 (p) REVERT: G 152 ARG cc_start: 0.6458 (mtm110) cc_final: 0.5136 (mpt90) REVERT: G 205 MET cc_start: 0.5279 (mmm) cc_final: 0.3403 (mtp) REVERT: H 87 ARG cc_start: 0.7921 (ptm-80) cc_final: 0.7559 (mmm160) REVERT: H 96 VAL cc_start: 0.8794 (m) cc_final: 0.8508 (t) REVERT: H 109 LYS cc_start: 0.9505 (mmtt) cc_final: 0.9305 (mmmt) REVERT: H 122 LEU cc_start: 0.8948 (pp) cc_final: 0.8369 (pp) REVERT: H 136 LYS cc_start: 0.8840 (ttpm) cc_final: 0.8513 (ttmt) REVERT: K 80 ILE cc_start: 0.9279 (mt) cc_final: 0.8750 (tt) REVERT: K 81 MET cc_start: 0.8650 (tpp) cc_final: 0.8355 (tpp) REVERT: K 89 CYS cc_start: 0.8946 (t) cc_final: 0.8381 (t) REVERT: K 110 GLU cc_start: 0.8496 (mp0) cc_final: 0.7955 (mp0) REVERT: L 51 CYS cc_start: 0.8893 (t) cc_final: 0.8689 (m) REVERT: L 66 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7199 (tm-30) REVERT: L 67 PHE cc_start: 0.8388 (m-80) cc_final: 0.8052 (m-80) REVERT: M 185 TYR cc_start: 0.7597 (p90) cc_final: 0.7118 (p90) REVERT: N 297 MET cc_start: 0.7398 (tmt) cc_final: 0.6793 (tmt) REVERT: N 311 THR cc_start: 0.7419 (p) cc_final: 0.7164 (t) REVERT: O 37 LEU cc_start: 0.8503 (tt) cc_final: 0.8168 (tp) REVERT: O 119 TYR cc_start: 0.7178 (m-80) cc_final: 0.6946 (m-10) REVERT: O 327 ARG cc_start: 0.7949 (tpt170) cc_final: 0.7669 (tpm170) REVERT: O 597 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7274 (tm-30) REVERT: P 23 MET cc_start: 0.6873 (mpm) cc_final: 0.6333 (mtt) REVERT: P 35 GLU cc_start: 0.6314 (pt0) cc_final: 0.5724 (tm-30) REVERT: P 63 LEU cc_start: 0.7639 (tt) cc_final: 0.7324 (tt) REVERT: P 250 ASP cc_start: 0.9037 (m-30) cc_final: 0.8608 (t0) REVERT: P 306 ASP cc_start: 0.7914 (t0) cc_final: 0.7677 (t0) REVERT: P 311 TYR cc_start: 0.9064 (m-10) cc_final: 0.8488 (m-10) REVERT: Q 66 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7638 (tptt) REVERT: U 63 ILE cc_start: 0.4074 (OUTLIER) cc_final: 0.3737 (tp) REVERT: U 111 THR cc_start: 0.6937 (t) cc_final: 0.5114 (t) REVERT: U 197 MET cc_start: 0.7262 (tpp) cc_final: 0.6216 (mmm) REVERT: U 221 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6848 (mm-30) REVERT: U 228 GLU cc_start: 0.7337 (mp0) cc_final: 0.7072 (tp30) REVERT: V 18 ASN cc_start: 0.8672 (t0) cc_final: 0.8195 (t0) REVERT: V 102 ASP cc_start: 0.8722 (p0) cc_final: 0.8000 (p0) REVERT: V 227 CYS cc_start: 0.8598 (p) cc_final: 0.8104 (t) REVERT: V 451 TYR cc_start: 0.7244 (m-80) cc_final: 0.6808 (m-80) REVERT: W 298 MET cc_start: 0.8329 (pmm) cc_final: 0.8034 (mtt) REVERT: W 439 PHE cc_start: 0.6195 (m-10) cc_final: 0.5864 (m-10) REVERT: W 497 ASP cc_start: 0.8546 (m-30) cc_final: 0.8325 (t0) REVERT: W 498 PHE cc_start: 0.6022 (m-10) cc_final: 0.5174 (m-80) REVERT: W 513 MET cc_start: 0.8671 (ttp) cc_final: 0.8422 (ttm) outliers start: 40 outliers final: 4 residues processed: 1137 average time/residue: 0.6605 time to fit residues: 1226.4547 Evaluate side-chains 624 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 619 time to evaluate : 5.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 481 optimal weight: 5.9990 chunk 432 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 291 optimal weight: 8.9990 chunk 230 optimal weight: 0.8980 chunk 446 optimal weight: 9.9990 chunk 172 optimal weight: 0.0370 chunk 271 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 517 optimal weight: 0.0770 overall best weight: 0.9218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 361 GLN A 367 ASN A 488 HIS A 520 HIS A 578 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** 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** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 GLN A1254 ASN A1318 HIS A1346 HIS A1354 HIS A1419 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 203 ASN B 225 HIS B 434 ASN B 456 HIS B 519 HIS B 577 HIS B 596 GLN B 600 HIS B 693 HIS B 821 HIS B 994 GLN B1029 HIS C 296 ASN E 3 GLN E 174 GLN F 78 GLN G 31 ASN H 21 ASN I 9 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 95 HIS L 53 HIS M 92 ASN M 141 ASN M 224 GLN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 549 GLN ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 HIS U 91 ASN ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 249 HIS V 473 HIS W 391 ASN W 509 HIS W 531 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 48905 Z= 0.191 Angle : 0.699 10.217 66567 Z= 0.363 Chirality : 0.045 0.279 7528 Planarity : 0.005 0.077 8090 Dihedral : 16.130 174.620 7646 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.71 % Favored : 92.27 % Rotamer: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % 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: -3.95 (0.09), residues: 5589 helix: -2.64 (0.10), residues: 1851 sheet: -2.15 (0.19), residues: 648 loop : -2.77 (0.10), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 88 HIS 0.016 0.001 HIS W 509 PHE 0.017 0.001 PHE K 63 TYR 0.019 0.001 TYR A 884 ARG 0.011 0.000 ARG O 40 *********************** 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 898 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 892 time to evaluate : 5.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7737 (t0) cc_final: 0.7332 (t0) REVERT: A 219 MET cc_start: 0.7345 (mtm) cc_final: 0.7037 (mtp) REVERT: A 273 MET cc_start: 0.5238 (mtp) cc_final: 0.4981 (ttp) REVERT: A 572 ASP cc_start: 0.8815 (p0) cc_final: 0.8614 (p0) REVERT: A 701 CYS cc_start: 0.8765 (m) cc_final: 0.8398 (t) REVERT: A 745 PHE cc_start: 0.7513 (p90) cc_final: 0.6690 (m-10) REVERT: A 765 LYS cc_start: 0.6566 (ttmm) cc_final: 0.6359 (tttt) REVERT: A 922 ASP cc_start: 0.7741 (m-30) cc_final: 0.7116 (m-30) REVERT: A 929 ASN cc_start: 0.8008 (m-40) cc_final: 0.7590 (t0) REVERT: A 985 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8132 (ttpt) REVERT: A 1028 MET cc_start: 0.6991 (mtp) cc_final: 0.6610 (mtt) REVERT: A 1145 LEU cc_start: 0.9168 (mm) cc_final: 0.8844 (mm) REVERT: A 1293 LEU cc_start: 0.8868 (tp) cc_final: 0.8648 (tp) REVERT: A 1343 MET cc_start: 0.8849 (mmt) cc_final: 0.8145 (mmm) REVERT: B 53 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8174 (mmtp) REVERT: B 122 ASP cc_start: 0.8682 (m-30) cc_final: 0.8405 (m-30) REVERT: B 358 MET cc_start: 0.8856 (mtp) cc_final: 0.8608 (mtp) REVERT: B 368 ASP cc_start: 0.8771 (p0) cc_final: 0.8567 (p0) REVERT: B 445 LYS cc_start: 0.8462 (tttp) cc_final: 0.8079 (tppt) REVERT: B 516 LEU cc_start: 0.9252 (tp) cc_final: 0.9050 (tp) REVERT: B 591 TYR cc_start: 0.7371 (t80) cc_final: 0.7043 (t80) REVERT: B 931 MET cc_start: 0.8638 (mpp) cc_final: 0.7954 (mpp) REVERT: B 941 ASP cc_start: 0.8728 (m-30) cc_final: 0.8318 (m-30) REVERT: B 953 MET cc_start: 0.8518 (mtt) cc_final: 0.8082 (mtp) REVERT: B 1068 ASP cc_start: 0.8306 (m-30) cc_final: 0.7874 (m-30) REVERT: B 1086 SER cc_start: 0.8848 (m) cc_final: 0.8575 (m) REVERT: B 1119 MET cc_start: 0.8268 (mtm) cc_final: 0.7732 (mtp) REVERT: B 1145 ASP cc_start: 0.8133 (p0) cc_final: 0.7785 (p0) REVERT: C 32 ASN cc_start: 0.8362 (t0) cc_final: 0.7819 (t0) REVERT: D 133 HIS cc_start: 0.5643 (t-90) cc_final: 0.5370 (t-170) REVERT: D 153 MET cc_start: 0.6633 (mtp) cc_final: 0.6229 (mtp) REVERT: E 90 VAL cc_start: 0.6006 (m) cc_final: 0.5623 (m) REVERT: E 99 HIS cc_start: 0.8239 (m-70) cc_final: 0.7863 (m170) REVERT: E 104 ASN cc_start: 0.7453 (t0) cc_final: 0.7158 (t0) REVERT: G 16 ASP cc_start: 0.8350 (p0) cc_final: 0.7802 (t0) REVERT: G 36 ASN cc_start: 0.7286 (t0) cc_final: 0.6998 (t0) REVERT: G 92 CYS cc_start: 0.5771 (m) cc_final: 0.5486 (p) REVERT: G 152 ARG cc_start: 0.6462 (mtm110) cc_final: 0.5053 (mpt90) REVERT: G 205 MET cc_start: 0.5217 (mmm) cc_final: 0.3377 (mtp) REVERT: H 87 ARG cc_start: 0.7919 (ptm-80) cc_final: 0.7684 (tpp80) REVERT: H 136 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8429 (ttmt) REVERT: J 64 ASN cc_start: 0.8499 (t0) cc_final: 0.8248 (p0) REVERT: K 81 MET cc_start: 0.8813 (tpp) cc_final: 0.8377 (tpp) REVERT: K 110 GLU cc_start: 0.8479 (mp0) cc_final: 0.7974 (mp0) REVERT: M 200 ARG cc_start: 0.7137 (mmp80) cc_final: 0.6816 (ptm-80) REVERT: N 312 ARG cc_start: 0.2987 (ptm160) cc_final: 0.2347 (ptp-170) REVERT: N 398 SER cc_start: 0.8294 (m) cc_final: 0.8033 (t) REVERT: N 421 GLN cc_start: 0.7659 (pm20) cc_final: 0.7315 (pt0) REVERT: O 89 ASP cc_start: 0.7827 (p0) cc_final: 0.7533 (p0) REVERT: O 109 GLU cc_start: 0.7370 (pp20) cc_final: 0.7168 (pp20) REVERT: O 128 HIS cc_start: 0.8900 (m170) cc_final: 0.8562 (m90) REVERT: O 240 GLN cc_start: 0.8552 (mt0) cc_final: 0.7486 (tp40) REVERT: P 35 GLU cc_start: 0.6571 (pt0) cc_final: 0.6142 (tm-30) REVERT: P 102 ARG cc_start: 0.7239 (mmp-170) cc_final: 0.6618 (mmp80) REVERT: P 299 MET cc_start: 0.8123 (mmm) cc_final: 0.7633 (mmp) REVERT: P 311 TYR cc_start: 0.8910 (m-10) cc_final: 0.8442 (m-10) REVERT: Q 66 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7705 (tptt) REVERT: U 111 THR cc_start: 0.6675 (t) cc_final: 0.5289 (m) REVERT: U 221 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6834 (mm-30) REVERT: V 18 ASN cc_start: 0.8651 (t0) cc_final: 0.8245 (t0) REVERT: V 98 GLU cc_start: 0.8465 (pp20) cc_final: 0.8093 (pp20) REVERT: V 102 ASP cc_start: 0.8526 (p0) cc_final: 0.8097 (p0) REVERT: V 134 CYS cc_start: 0.9127 (m) cc_final: 0.8887 (m) REVERT: V 137 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8320 (tm-30) REVERT: V 169 HIS cc_start: 0.8392 (m-70) cc_final: 0.8065 (m90) REVERT: V 227 CYS cc_start: 0.8562 (p) cc_final: 0.8260 (t) REVERT: W 293 PHE cc_start: 0.8439 (p90) cc_final: 0.8143 (p90) REVERT: W 300 LYS cc_start: 0.7755 (pttp) cc_final: 0.7076 (mtpt) REVERT: W 439 PHE cc_start: 0.6441 (m-10) cc_final: 0.5931 (m-10) REVERT: W 498 PHE cc_start: 0.6041 (m-10) cc_final: 0.5108 (m-80) REVERT: W 509 HIS cc_start: 0.9118 (m90) cc_final: 0.8888 (m-70) outliers start: 6 outliers final: 2 residues processed: 894 average time/residue: 0.5632 time to fit residues: 840.9593 Evaluate side-chains 580 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 578 time to evaluate : 5.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 287 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 430 optimal weight: 6.9990 chunk 352 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 518 optimal weight: 5.9990 chunk 560 optimal weight: 10.0000 chunk 461 optimal weight: 5.9990 chunk 514 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 416 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 207 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 HIS A 899 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN B 880 HIS B 883 GLN B1014 GLN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 GLN C 207 HIS C 296 ASN D 125 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN G 28 HIS ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 HIS P 258 HIS V 35 ASN ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 256 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 48905 Z= 0.327 Angle : 0.738 10.022 66567 Z= 0.389 Chirality : 0.047 0.279 7528 Planarity : 0.005 0.067 8090 Dihedral : 16.062 177.873 7646 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.00 % Favored : 89.98 % Rotamer: Outliers : 0.14 % Allowed : 6.67 % Favored : 93.19 % 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: -3.38 (0.10), residues: 5589 helix: -1.84 (0.11), residues: 1904 sheet: -2.10 (0.19), residues: 643 loop : -2.60 (0.10), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 140 HIS 0.010 0.002 HIS A 92 PHE 0.036 0.002 PHE P 142 TYR 0.023 0.002 TYR F 84 ARG 0.010 0.001 ARG O 567 *********************** 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 748 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 741 time to evaluate : 5.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7606 (t0) cc_final: 0.6753 (t0) REVERT: A 138 MET cc_start: 0.8610 (mtm) cc_final: 0.8188 (ptp) REVERT: A 273 MET cc_start: 0.5586 (mtp) cc_final: 0.5253 (ttp) REVERT: A 550 ILE cc_start: 0.8957 (pt) cc_final: 0.8734 (pt) REVERT: A 745 PHE cc_start: 0.7770 (p90) cc_final: 0.6955 (m-10) REVERT: A 762 LEU cc_start: 0.8396 (pt) cc_final: 0.7235 (mm) REVERT: A 863 PHE cc_start: 0.8773 (m-80) cc_final: 0.8535 (m-80) REVERT: A 922 ASP cc_start: 0.8040 (m-30) cc_final: 0.7544 (m-30) REVERT: A 987 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8105 (pm20) REVERT: A 1028 MET cc_start: 0.7165 (mtp) cc_final: 0.6736 (mtt) REVERT: A 1145 LEU cc_start: 0.9178 (mm) cc_final: 0.8860 (mm) REVERT: A 1293 LEU cc_start: 0.8762 (tp) cc_final: 0.8531 (tp) REVERT: A 1343 MET cc_start: 0.9032 (mmt) cc_final: 0.8765 (mmt) REVERT: B 53 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8325 (mmtp) REVERT: B 122 ASP cc_start: 0.8940 (m-30) cc_final: 0.8661 (m-30) REVERT: B 358 MET cc_start: 0.8753 (mtp) cc_final: 0.8537 (mtp) REVERT: B 378 GLU cc_start: 0.8847 (pp20) cc_final: 0.8597 (pp20) REVERT: B 445 LYS cc_start: 0.8484 (tttp) cc_final: 0.8065 (tppt) REVERT: B 516 LEU cc_start: 0.9371 (tp) cc_final: 0.9148 (tp) REVERT: B 591 TYR cc_start: 0.7589 (t80) cc_final: 0.7222 (t80) REVERT: B 705 MET cc_start: 0.7299 (mtt) cc_final: 0.7039 (mtt) REVERT: B 931 MET cc_start: 0.8697 (mpp) cc_final: 0.7929 (mpp) REVERT: B 941 ASP cc_start: 0.8400 (m-30) cc_final: 0.8154 (m-30) REVERT: B 953 MET cc_start: 0.8368 (mtt) cc_final: 0.8041 (mtt) REVERT: B 1073 TYR cc_start: 0.8716 (m-10) cc_final: 0.8484 (m-80) REVERT: B 1081 GLU cc_start: 0.8507 (pp20) cc_final: 0.8257 (pp20) REVERT: B 1086 SER cc_start: 0.9204 (m) cc_final: 0.8887 (m) REVERT: B 1119 MET cc_start: 0.8470 (mtm) cc_final: 0.7729 (mtp) REVERT: B 1145 ASP cc_start: 0.8112 (p0) cc_final: 0.7823 (p0) REVERT: C 32 ASN cc_start: 0.8555 (t0) cc_final: 0.8075 (t0) REVERT: D 131 MET cc_start: 0.6068 (tpp) cc_final: 0.5651 (mmm) REVERT: D 152 GLU cc_start: 0.5513 (tm-30) cc_final: 0.5313 (tp30) REVERT: D 153 MET cc_start: 0.6646 (mtp) cc_final: 0.6299 (mtp) REVERT: E 22 MET cc_start: 0.9139 (tmm) cc_final: 0.8897 (tmm) REVERT: E 57 MET cc_start: 0.7177 (tpp) cc_final: 0.6902 (tpp) REVERT: E 75 MET cc_start: 0.7331 (ppp) cc_final: 0.6861 (ppp) REVERT: E 95 THR cc_start: 0.8551 (p) cc_final: 0.8302 (p) REVERT: E 99 HIS cc_start: 0.8388 (m-70) cc_final: 0.7860 (m90) REVERT: G 36 ASN cc_start: 0.7490 (t0) cc_final: 0.7126 (t0) REVERT: G 92 CYS cc_start: 0.6114 (m) cc_final: 0.5846 (p) REVERT: G 152 ARG cc_start: 0.6354 (mtm110) cc_final: 0.4804 (mpt90) REVERT: H 122 LEU cc_start: 0.9123 (pp) cc_final: 0.8900 (pp) REVERT: H 136 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8530 (ttmt) REVERT: I 1 MET cc_start: 0.7370 (ppp) cc_final: 0.6552 (ppp) REVERT: K 81 MET cc_start: 0.8844 (tpp) cc_final: 0.8435 (tpp) REVERT: K 110 GLU cc_start: 0.8618 (mp0) cc_final: 0.8107 (mp0) REVERT: L 67 PHE cc_start: 0.8518 (m-80) cc_final: 0.8275 (m-10) REVERT: M 200 ARG cc_start: 0.7256 (mmp80) cc_final: 0.6830 (ptm-80) REVERT: N 398 SER cc_start: 0.8602 (m) cc_final: 0.8187 (t) REVERT: N 421 GLN cc_start: 0.7877 (pm20) cc_final: 0.7245 (pt0) REVERT: O 105 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8745 (mtpt) REVERT: O 128 HIS cc_start: 0.8936 (m170) cc_final: 0.8599 (m90) REVERT: O 240 GLN cc_start: 0.8626 (mt0) cc_final: 0.7570 (tp40) REVERT: O 345 PHE cc_start: 0.8155 (m-80) cc_final: 0.7900 (m-80) REVERT: O 541 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.8984 (tp) REVERT: O 597 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7455 (mm-40) REVERT: P 35 GLU cc_start: 0.6694 (pt0) cc_final: 0.6173 (tm-30) REVERT: P 102 ARG cc_start: 0.7203 (mmp-170) cc_final: 0.6518 (mmp80) REVERT: P 311 TYR cc_start: 0.8996 (m-10) cc_final: 0.8552 (m-10) REVERT: Q 66 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7770 (tptt) REVERT: U 111 THR cc_start: 0.6803 (t) cc_final: 0.5386 (m) REVERT: U 139 TYR cc_start: 0.7314 (m-10) cc_final: 0.6971 (m-10) REVERT: V 18 ASN cc_start: 0.8799 (t0) cc_final: 0.8277 (t0) REVERT: V 98 GLU cc_start: 0.8571 (pp20) cc_final: 0.8340 (pp20) REVERT: V 102 ASP cc_start: 0.8502 (p0) cc_final: 0.8096 (p0) REVERT: V 134 CYS cc_start: 0.9215 (m) cc_final: 0.8932 (m) REVERT: V 137 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8362 (tm-30) REVERT: V 142 MET cc_start: 0.9166 (tmm) cc_final: 0.8938 (tmm) REVERT: V 169 HIS cc_start: 0.8330 (m-70) cc_final: 0.8000 (m90) REVERT: W 429 TYR cc_start: 0.7174 (m-10) cc_final: 0.6934 (m-10) REVERT: W 432 LEU cc_start: 0.7907 (pp) cc_final: 0.7467 (tt) REVERT: W 441 LEU cc_start: 0.8636 (pt) cc_final: 0.8344 (pt) outliers start: 7 outliers final: 3 residues processed: 748 average time/residue: 0.5790 time to fit residues: 731.8990 Evaluate side-chains 531 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 527 time to evaluate : 5.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 512 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 269 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 247 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 520 optimal weight: 3.9990 chunk 550 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 493 optimal weight: 10.0000 chunk 148 optimal weight: 0.0970 overall best weight: 1.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 HIS ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN B 883 GLN ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN H 21 ASN H 139 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 584 ASN ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 119 HIS P 189 ASN U 179 HIS ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 235 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 48905 Z= 0.190 Angle : 0.662 10.527 66567 Z= 0.339 Chirality : 0.045 0.305 7528 Planarity : 0.004 0.055 8090 Dihedral : 15.905 178.652 7646 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -3.04 (0.10), residues: 5589 helix: -1.40 (0.11), residues: 1904 sheet: -1.90 (0.19), residues: 632 loop : -2.51 (0.10), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 140 HIS 0.010 0.001 HIS W 509 PHE 0.029 0.001 PHE P 142 TYR 0.023 0.001 TYR B 658 ARG 0.012 0.000 ARG V 149 *********************** 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 744 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 744 time to evaluate : 5.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7554 (t0) cc_final: 0.6518 (t0) REVERT: A 138 MET cc_start: 0.8534 (mtm) cc_final: 0.8073 (ptp) REVERT: A 142 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8493 (pttp) REVERT: A 273 MET cc_start: 0.5672 (mtp) cc_final: 0.5275 (ttp) REVERT: A 483 LEU cc_start: 0.9449 (tp) cc_final: 0.9162 (tp) REVERT: A 582 MET cc_start: 0.8704 (mtm) cc_final: 0.8478 (mtp) REVERT: A 745 PHE cc_start: 0.7784 (p90) cc_final: 0.6999 (m-10) REVERT: A 762 LEU cc_start: 0.8267 (pt) cc_final: 0.7031 (mm) REVERT: A 863 PHE cc_start: 0.8759 (m-80) cc_final: 0.8313 (m-80) REVERT: A 922 ASP cc_start: 0.7995 (m-30) cc_final: 0.7421 (m-30) REVERT: A 987 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8123 (pm20) REVERT: A 1028 MET cc_start: 0.7090 (mtp) cc_final: 0.6671 (mtt) REVERT: A 1343 MET cc_start: 0.8957 (mmt) cc_final: 0.8116 (mmm) REVERT: B 53 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8351 (mmtp) REVERT: B 122 ASP cc_start: 0.8880 (m-30) cc_final: 0.8631 (m-30) REVERT: B 378 GLU cc_start: 0.8691 (pp20) cc_final: 0.8451 (pp20) REVERT: B 445 LYS cc_start: 0.8343 (tttp) cc_final: 0.8038 (tppt) REVERT: B 516 LEU cc_start: 0.9357 (tp) cc_final: 0.9136 (tp) REVERT: B 591 TYR cc_start: 0.7635 (t80) cc_final: 0.7199 (t80) REVERT: B 931 MET cc_start: 0.8634 (mpp) cc_final: 0.7850 (mpp) REVERT: B 941 ASP cc_start: 0.8467 (m-30) cc_final: 0.8250 (m-30) REVERT: B 953 MET cc_start: 0.8341 (mtt) cc_final: 0.8028 (mtt) REVERT: B 1068 ASP cc_start: 0.8520 (m-30) cc_final: 0.8248 (m-30) REVERT: B 1069 CYS cc_start: 0.8360 (t) cc_final: 0.8130 (p) REVERT: B 1073 TYR cc_start: 0.8644 (m-10) cc_final: 0.8057 (m-10) REVERT: B 1119 MET cc_start: 0.8429 (mtm) cc_final: 0.7562 (mtp) REVERT: B 1145 ASP cc_start: 0.8292 (p0) cc_final: 0.7884 (p0) REVERT: C 32 ASN cc_start: 0.8555 (t0) cc_final: 0.8026 (t0) REVERT: D 131 MET cc_start: 0.6477 (tpp) cc_final: 0.6208 (mmm) REVERT: D 152 GLU cc_start: 0.5509 (tm-30) cc_final: 0.5308 (tp30) REVERT: D 153 MET cc_start: 0.6804 (mtp) cc_final: 0.6467 (mtp) REVERT: E 22 MET cc_start: 0.9127 (tmm) cc_final: 0.8608 (tmm) REVERT: E 57 MET cc_start: 0.7214 (tpp) cc_final: 0.6949 (tpp) REVERT: E 75 MET cc_start: 0.7157 (ppp) cc_final: 0.6920 (ppp) REVERT: E 95 THR cc_start: 0.8749 (p) cc_final: 0.8333 (p) REVERT: E 99 HIS cc_start: 0.8347 (m-70) cc_final: 0.7798 (m90) REVERT: E 204 THR cc_start: 0.8315 (m) cc_final: 0.8041 (t) REVERT: G 36 ASN cc_start: 0.7596 (t0) cc_final: 0.7354 (t0) REVERT: G 152 ARG cc_start: 0.6252 (mtm110) cc_final: 0.4639 (mpt90) REVERT: H 87 ARG cc_start: 0.7870 (ptm-80) cc_final: 0.7544 (mmm160) REVERT: H 122 LEU cc_start: 0.9173 (pp) cc_final: 0.8888 (pp) REVERT: H 136 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8504 (ttmt) REVERT: H 138 GLU cc_start: 0.8450 (pm20) cc_final: 0.8065 (tp30) REVERT: I 1 MET cc_start: 0.7811 (ppp) cc_final: 0.7177 (ppp) REVERT: I 11 MET cc_start: 0.8251 (tpp) cc_final: 0.8015 (tpt) REVERT: K 81 MET cc_start: 0.8772 (tpp) cc_final: 0.8411 (tpp) REVERT: K 110 GLU cc_start: 0.8626 (mp0) cc_final: 0.8066 (mp0) REVERT: K 125 MET cc_start: 0.9186 (mmm) cc_final: 0.8864 (mmm) REVERT: K 129 ASP cc_start: 0.8604 (t70) cc_final: 0.8223 (t70) REVERT: K 132 GLU cc_start: 0.8586 (tt0) cc_final: 0.8264 (tm-30) REVERT: L 66 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8391 (tm-30) REVERT: M 90 TYR cc_start: 0.7263 (m-80) cc_final: 0.7031 (m-80) REVERT: M 194 LYS cc_start: 0.7709 (tmtt) cc_final: 0.7196 (mtmm) REVERT: M 200 ARG cc_start: 0.7220 (mmp80) cc_final: 0.6845 (ptm-80) REVERT: N 398 SER cc_start: 0.8689 (m) cc_final: 0.8268 (t) REVERT: N 421 GLN cc_start: 0.7544 (pm20) cc_final: 0.7010 (pt0) REVERT: O 128 HIS cc_start: 0.8711 (m170) cc_final: 0.8433 (m90) REVERT: O 183 MET cc_start: 0.8542 (mpp) cc_final: 0.8318 (mpp) REVERT: O 240 GLN cc_start: 0.8431 (mt0) cc_final: 0.7557 (tp40) REVERT: P 19 HIS cc_start: 0.8636 (p-80) cc_final: 0.8259 (p-80) REVERT: P 35 GLU cc_start: 0.6646 (pt0) cc_final: 0.6212 (tm-30) REVERT: P 102 ARG cc_start: 0.6986 (mmp-170) cc_final: 0.6423 (mmp80) REVERT: P 299 MET cc_start: 0.7993 (mmm) cc_final: 0.7669 (mmp) REVERT: P 311 TYR cc_start: 0.8951 (m-10) cc_final: 0.8541 (m-10) REVERT: Q 66 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7685 (tptt) REVERT: Q 67 ASP cc_start: 0.7597 (p0) cc_final: 0.7387 (p0) REVERT: U 111 THR cc_start: 0.6787 (t) cc_final: 0.5315 (m) REVERT: U 139 TYR cc_start: 0.7199 (m-10) cc_final: 0.6799 (m-10) REVERT: V 18 ASN cc_start: 0.8834 (t0) cc_final: 0.8250 (t0) REVERT: V 98 GLU cc_start: 0.8443 (pp20) cc_final: 0.7945 (pp20) REVERT: V 102 ASP cc_start: 0.8445 (p0) cc_final: 0.7872 (p0) REVERT: V 123 GLN cc_start: 0.8447 (pm20) cc_final: 0.8208 (pp30) REVERT: V 137 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8304 (tm-30) REVERT: V 151 GLN cc_start: 0.8872 (mt0) cc_final: 0.8629 (mp10) REVERT: V 169 HIS cc_start: 0.8338 (m-70) cc_final: 0.7995 (m90) REVERT: V 257 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8431 (tm-30) REVERT: W 429 TYR cc_start: 0.7315 (m-10) cc_final: 0.7102 (m-80) REVERT: W 432 LEU cc_start: 0.7767 (pp) cc_final: 0.7360 (tt) REVERT: W 441 LEU cc_start: 0.8528 (pt) cc_final: 0.8246 (pt) REVERT: W 444 GLN cc_start: 0.8225 (mp10) cc_final: 0.7921 (mp10) REVERT: W 498 PHE cc_start: 0.6305 (m-80) cc_final: 0.5283 (m-80) outliers start: 0 outliers final: 0 residues processed: 744 average time/residue: 0.5501 time to fit residues: 694.9743 Evaluate side-chains 532 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 458 optimal weight: 10.0000 chunk 312 optimal weight: 0.0570 chunk 8 optimal weight: 9.9990 chunk 410 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 470 optimal weight: 3.9990 chunk 380 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 494 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 355 GLN A 425 ASN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN A 931 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 GLN ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN B 883 GLN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN G 28 HIS H 21 ASN H 139 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 298 ASN ** O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 544 ASN ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 179 HIS ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 509 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 48905 Z= 0.345 Angle : 0.728 10.221 66567 Z= 0.379 Chirality : 0.047 0.298 7528 Planarity : 0.005 0.057 8090 Dihedral : 15.909 178.765 7646 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.57 % Favored : 89.41 % Rotamer: Outliers : 0.02 % Allowed : 5.07 % Favored : 94.91 % 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: -2.93 (0.10), residues: 5589 helix: -1.22 (0.11), residues: 1937 sheet: -1.88 (0.19), residues: 641 loop : -2.50 (0.10), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 185 HIS 0.021 0.002 HIS W 509 PHE 0.027 0.002 PHE P 142 TYR 0.022 0.002 TYR C 157 ARG 0.010 0.001 ARG A 482 *********************** 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 688 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 687 time to evaluate : 6.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.9134 (pp30) cc_final: 0.8894 (pp30) REVERT: A 134 ASN cc_start: 0.7442 (t0) cc_final: 0.6860 (t0) REVERT: A 138 MET cc_start: 0.8548 (mtm) cc_final: 0.8304 (mtp) REVERT: A 161 ASN cc_start: 0.8625 (m-40) cc_final: 0.8341 (t0) REVERT: A 273 MET cc_start: 0.5645 (mtp) cc_final: 0.5144 (ttm) REVERT: A 480 LEU cc_start: 0.8952 (mt) cc_final: 0.8744 (mp) REVERT: A 572 ASP cc_start: 0.8867 (p0) cc_final: 0.8655 (p0) REVERT: A 832 LEU cc_start: 0.8838 (mt) cc_final: 0.8315 (mp) REVERT: A 863 PHE cc_start: 0.8758 (m-80) cc_final: 0.8396 (m-80) REVERT: A 922 ASP cc_start: 0.8250 (m-30) cc_final: 0.7676 (m-30) REVERT: A 1028 MET cc_start: 0.7136 (mtp) cc_final: 0.6759 (mtt) REVERT: A 1343 MET cc_start: 0.8994 (mmt) cc_final: 0.7931 (mmm) REVERT: B 53 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8434 (mmtp) REVERT: B 122 ASP cc_start: 0.8969 (m-30) cc_final: 0.8753 (m-30) REVERT: B 358 MET cc_start: 0.8772 (mtp) cc_final: 0.8531 (mtp) REVERT: B 364 LYS cc_start: 0.8893 (tptp) cc_final: 0.8659 (tppt) REVERT: B 445 LYS cc_start: 0.8662 (tttp) cc_final: 0.8316 (tppt) REVERT: B 567 PHE cc_start: 0.8119 (p90) cc_final: 0.7532 (p90) REVERT: B 591 TYR cc_start: 0.7814 (t80) cc_final: 0.7482 (t80) REVERT: B 931 MET cc_start: 0.8596 (mpp) cc_final: 0.8118 (mpp) REVERT: B 953 MET cc_start: 0.8446 (mtt) cc_final: 0.8094 (mtt) REVERT: B 1068 ASP cc_start: 0.8485 (m-30) cc_final: 0.8197 (m-30) REVERT: B 1119 MET cc_start: 0.8548 (mtm) cc_final: 0.7656 (mtp) REVERT: B 1145 ASP cc_start: 0.8322 (p0) cc_final: 0.7956 (p0) REVERT: C 32 ASN cc_start: 0.8625 (t0) cc_final: 0.8103 (t0) REVERT: D 152 GLU cc_start: 0.5644 (tm-30) cc_final: 0.5302 (tp30) REVERT: D 153 MET cc_start: 0.6539 (mtp) cc_final: 0.6337 (mtp) REVERT: E 22 MET cc_start: 0.9253 (tmm) cc_final: 0.8835 (tmm) REVERT: E 57 MET cc_start: 0.7334 (tpp) cc_final: 0.6662 (tmm) REVERT: E 75 MET cc_start: 0.7166 (ppp) cc_final: 0.6601 (ppp) REVERT: E 95 THR cc_start: 0.8642 (p) cc_final: 0.8375 (p) REVERT: E 99 HIS cc_start: 0.8476 (m-70) cc_final: 0.7982 (m90) REVERT: E 104 ASN cc_start: 0.7908 (t0) cc_final: 0.7600 (t0) REVERT: G 28 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.6820 (t-90) REVERT: G 36 ASN cc_start: 0.7770 (t0) cc_final: 0.7275 (t0) REVERT: G 152 ARG cc_start: 0.6525 (mtm110) cc_final: 0.4928 (mpt90) REVERT: H 110 ASP cc_start: 0.9031 (p0) cc_final: 0.8528 (t0) REVERT: H 136 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8627 (ttmt) REVERT: H 138 GLU cc_start: 0.8600 (pm20) cc_final: 0.8125 (tp30) REVERT: I 1 MET cc_start: 0.6829 (ppp) cc_final: 0.6358 (ppp) REVERT: J 52 THR cc_start: 0.8995 (p) cc_final: 0.8722 (p) REVERT: K 81 MET cc_start: 0.8781 (tpp) cc_final: 0.8375 (tpp) REVERT: K 110 GLU cc_start: 0.8629 (mp0) cc_final: 0.8051 (mp0) REVERT: K 129 ASP cc_start: 0.8605 (t70) cc_final: 0.8255 (t70) REVERT: K 132 GLU cc_start: 0.8651 (tt0) cc_final: 0.8442 (tm-30) REVERT: L 66 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8553 (tm-30) REVERT: M 194 LYS cc_start: 0.7808 (tmtt) cc_final: 0.7191 (mttp) REVERT: M 200 ARG cc_start: 0.7271 (mmp80) cc_final: 0.6884 (tmm-80) REVERT: N 398 SER cc_start: 0.8858 (m) cc_final: 0.8548 (t) REVERT: N 419 THR cc_start: 0.8325 (m) cc_final: 0.8123 (p) REVERT: N 421 GLN cc_start: 0.7614 (pm20) cc_final: 0.6379 (pt0) REVERT: O 67 MET cc_start: 0.8710 (mmm) cc_final: 0.8474 (mmm) REVERT: O 105 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8693 (mtpt) REVERT: O 128 HIS cc_start: 0.9006 (m170) cc_final: 0.8619 (m90) REVERT: O 240 GLN cc_start: 0.8562 (mt0) cc_final: 0.7516 (tp40) REVERT: O 510 CYS cc_start: 0.7408 (t) cc_final: 0.7156 (t) REVERT: P 35 GLU cc_start: 0.6735 (pt0) cc_final: 0.6271 (tm-30) REVERT: P 68 ASP cc_start: 0.7575 (t0) cc_final: 0.7303 (t0) REVERT: P 102 ARG cc_start: 0.6917 (mmp-170) cc_final: 0.6249 (mmp80) REVERT: P 295 ASN cc_start: 0.8370 (m110) cc_final: 0.8170 (m-40) REVERT: P 311 TYR cc_start: 0.8996 (m-10) cc_final: 0.8643 (m-10) REVERT: U 111 THR cc_start: 0.7002 (t) cc_final: 0.5683 (m) REVERT: U 139 TYR cc_start: 0.7229 (m-10) cc_final: 0.6721 (m-10) REVERT: V 18 ASN cc_start: 0.8878 (t0) cc_final: 0.8362 (t0) REVERT: V 98 GLU cc_start: 0.8532 (pp20) cc_final: 0.8244 (pp20) REVERT: V 102 ASP cc_start: 0.8632 (p0) cc_final: 0.8304 (p0) REVERT: V 137 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8434 (tm-30) REVERT: V 169 HIS cc_start: 0.8420 (m-70) cc_final: 0.8090 (m90) REVERT: V 257 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8502 (tm-30) REVERT: W 432 LEU cc_start: 0.7698 (pp) cc_final: 0.7495 (pp) REVERT: W 441 LEU cc_start: 0.8678 (pt) cc_final: 0.8327 (pt) REVERT: W 444 GLN cc_start: 0.8121 (mp10) cc_final: 0.7886 (mp10) REVERT: W 498 PHE cc_start: 0.6173 (m-80) cc_final: 0.5531 (m-80) outliers start: 1 outliers final: 0 residues processed: 688 average time/residue: 0.5462 time to fit residues: 638.2829 Evaluate side-chains 518 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 517 time to evaluate : 4.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 185 optimal weight: 0.9990 chunk 496 optimal weight: 6.9990 chunk 108 optimal weight: 0.3980 chunk 323 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 551 optimal weight: 4.9990 chunk 457 optimal weight: 10.0000 chunk 255 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 289 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN H 139 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 119 HIS ** P 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 ASN ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 391 ASN W 509 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 48905 Z= 0.179 Angle : 0.659 10.826 66567 Z= 0.334 Chirality : 0.045 0.428 7528 Planarity : 0.004 0.044 8090 Dihedral : 15.803 178.077 7646 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.57 % 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: -2.66 (0.11), residues: 5589 helix: -0.91 (0.12), residues: 1933 sheet: -1.75 (0.19), residues: 632 loop : -2.41 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 819 HIS 0.015 0.001 HIS W 509 PHE 0.020 0.001 PHE P 142 TYR 0.015 0.001 TYR V 92 ARG 0.010 0.000 ARG C 11 *********************** 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 731 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 730 time to evaluate : 5.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7380 (t0) cc_final: 0.6777 (t0) REVERT: A 138 MET cc_start: 0.8640 (mtm) cc_final: 0.8397 (mtp) REVERT: A 142 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8647 (pttp) REVERT: A 161 ASN cc_start: 0.8578 (m-40) cc_final: 0.8046 (t0) REVERT: A 188 LYS cc_start: 0.7695 (tppt) cc_final: 0.7488 (tppt) REVERT: A 273 MET cc_start: 0.5538 (mtp) cc_final: 0.4941 (ttm) REVERT: A 572 ASP cc_start: 0.8815 (p0) cc_final: 0.8606 (p0) REVERT: A 582 MET cc_start: 0.8750 (mtm) cc_final: 0.8549 (mtp) REVERT: A 665 ASP cc_start: 0.7756 (p0) cc_final: 0.6959 (p0) REVERT: A 697 MET cc_start: 0.9381 (tmm) cc_final: 0.9174 (tmm) REVERT: A 762 LEU cc_start: 0.8248 (pp) cc_final: 0.7335 (mm) REVERT: A 863 PHE cc_start: 0.8689 (m-80) cc_final: 0.8311 (m-80) REVERT: A 890 MET cc_start: 0.8876 (tpt) cc_final: 0.8593 (tpp) REVERT: A 987 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8061 (pm20) REVERT: A 1028 MET cc_start: 0.7003 (mtp) cc_final: 0.6627 (mtt) REVERT: A 1084 GLU cc_start: 0.8837 (pm20) cc_final: 0.8625 (pm20) REVERT: A 1343 MET cc_start: 0.8877 (mmt) cc_final: 0.7728 (mmm) REVERT: B 53 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8407 (mmtm) REVERT: B 122 ASP cc_start: 0.8960 (m-30) cc_final: 0.8735 (m-30) REVERT: B 358 MET cc_start: 0.8869 (mtp) cc_final: 0.8429 (mtp) REVERT: B 364 LYS cc_start: 0.8871 (tptp) cc_final: 0.8616 (tppt) REVERT: B 445 LYS cc_start: 0.8607 (tttp) cc_final: 0.8270 (tppt) REVERT: B 470 MET cc_start: 0.8894 (mmm) cc_final: 0.7954 (mmm) REVERT: B 516 LEU cc_start: 0.9331 (tp) cc_final: 0.9127 (tp) REVERT: B 517 MET cc_start: 0.8748 (mmt) cc_final: 0.8000 (mmm) REVERT: B 567 PHE cc_start: 0.7991 (p90) cc_final: 0.7553 (p90) REVERT: B 766 ASP cc_start: 0.7992 (p0) cc_final: 0.7336 (p0) REVERT: B 885 MET cc_start: 0.8703 (tmm) cc_final: 0.8479 (tmm) REVERT: B 931 MET cc_start: 0.8590 (mpp) cc_final: 0.7828 (mpp) REVERT: B 944 MET cc_start: 0.8024 (ptm) cc_final: 0.7686 (ptp) REVERT: B 953 MET cc_start: 0.8370 (mtt) cc_final: 0.8047 (mtt) REVERT: B 1068 ASP cc_start: 0.8307 (m-30) cc_final: 0.7867 (m-30) REVERT: B 1073 TYR cc_start: 0.8844 (m-10) cc_final: 0.8019 (m-10) REVERT: B 1119 MET cc_start: 0.8461 (mtm) cc_final: 0.7584 (mtp) REVERT: B 1145 ASP cc_start: 0.8305 (p0) cc_final: 0.7866 (p0) REVERT: C 32 ASN cc_start: 0.8606 (t0) cc_final: 0.8069 (t0) REVERT: D 153 MET cc_start: 0.6717 (mtp) cc_final: 0.6429 (mtp) REVERT: E 57 MET cc_start: 0.7283 (tpp) cc_final: 0.6565 (tmm) REVERT: E 95 THR cc_start: 0.8896 (p) cc_final: 0.8456 (p) REVERT: E 99 HIS cc_start: 0.8325 (m-70) cc_final: 0.8086 (m90) REVERT: E 104 ASN cc_start: 0.7827 (t0) cc_final: 0.7514 (t0) REVERT: E 204 THR cc_start: 0.8052 (m) cc_final: 0.7681 (t) REVERT: F 151 LEU cc_start: 0.9245 (mm) cc_final: 0.8688 (mt) REVERT: G 36 ASN cc_start: 0.7677 (t0) cc_final: 0.7266 (t0) REVERT: G 152 ARG cc_start: 0.6523 (mtm110) cc_final: 0.4906 (mpt90) REVERT: H 110 ASP cc_start: 0.8957 (p0) cc_final: 0.8486 (t0) REVERT: H 136 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8575 (ttmt) REVERT: H 138 GLU cc_start: 0.8454 (pm20) cc_final: 0.8066 (tp30) REVERT: I 1 MET cc_start: 0.6875 (ppp) cc_final: 0.6249 (ppp) REVERT: I 11 MET cc_start: 0.8108 (tpp) cc_final: 0.7881 (tpt) REVERT: K 110 GLU cc_start: 0.8617 (mp0) cc_final: 0.8005 (mp0) REVERT: K 129 ASP cc_start: 0.8659 (t70) cc_final: 0.8335 (t70) REVERT: K 132 GLU cc_start: 0.8664 (tt0) cc_final: 0.8455 (tm-30) REVERT: M 165 ASP cc_start: 0.6217 (m-30) cc_final: 0.5730 (m-30) REVERT: M 166 MET cc_start: 0.7745 (mpp) cc_final: 0.7456 (mpp) REVERT: M 194 LYS cc_start: 0.7771 (tmtt) cc_final: 0.7238 (mttt) REVERT: M 200 ARG cc_start: 0.7152 (mmp80) cc_final: 0.6898 (ptm-80) REVERT: N 398 SER cc_start: 0.8870 (m) cc_final: 0.8569 (t) REVERT: N 421 GLN cc_start: 0.6431 (pm20) cc_final: 0.6162 (pt0) REVERT: O 128 HIS cc_start: 0.8885 (m170) cc_final: 0.8180 (m90) REVERT: O 240 GLN cc_start: 0.8410 (mt0) cc_final: 0.7522 (tp40) REVERT: O 345 PHE cc_start: 0.8128 (m-80) cc_final: 0.7682 (m-80) REVERT: P 35 GLU cc_start: 0.6660 (pt0) cc_final: 0.6254 (tm-30) REVERT: P 68 ASP cc_start: 0.7524 (t0) cc_final: 0.7252 (t0) REVERT: P 102 ARG cc_start: 0.6835 (mmp-170) cc_final: 0.6396 (mmp-170) REVERT: P 179 LEU cc_start: 0.8966 (tt) cc_final: 0.8628 (mt) REVERT: P 295 ASN cc_start: 0.8385 (m110) cc_final: 0.8149 (m-40) REVERT: P 299 MET cc_start: 0.7978 (mmm) cc_final: 0.7705 (mmp) REVERT: P 311 TYR cc_start: 0.8932 (m-10) cc_final: 0.8600 (m-10) REVERT: U 111 THR cc_start: 0.7071 (t) cc_final: 0.5734 (m) REVERT: U 139 TYR cc_start: 0.7181 (m-10) cc_final: 0.6610 (m-10) REVERT: V 18 ASN cc_start: 0.8867 (t0) cc_final: 0.8277 (t0) REVERT: V 98 GLU cc_start: 0.8363 (pp20) cc_final: 0.7859 (pp20) REVERT: V 102 ASP cc_start: 0.8503 (p0) cc_final: 0.8080 (p0) REVERT: V 257 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8482 (tm-30) REVERT: W 432 LEU cc_start: 0.7686 (pp) cc_final: 0.7062 (tt) REVERT: W 441 LEU cc_start: 0.8563 (pt) cc_final: 0.8208 (pt) REVERT: W 444 GLN cc_start: 0.8266 (mp10) cc_final: 0.7895 (mp10) REVERT: W 498 PHE cc_start: 0.6095 (m-80) cc_final: 0.5407 (m-80) REVERT: W 509 HIS cc_start: 0.9175 (m90) cc_final: 0.8951 (m-70) outliers start: 1 outliers final: 1 residues processed: 731 average time/residue: 0.5581 time to fit residues: 694.8795 Evaluate side-chains 537 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 536 time to evaluate : 5.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 531 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 402 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 464 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 549 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 334 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 HIS B 596 GLN B 754 ASN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN H 139 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN N 287 HIS N 298 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 20 ASN V 35 ASN ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 48905 Z= 0.294 Angle : 0.706 11.001 66567 Z= 0.364 Chirality : 0.046 0.260 7528 Planarity : 0.004 0.051 8090 Dihedral : 15.806 178.377 7646 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -2.65 (0.11), residues: 5589 helix: -0.89 (0.12), residues: 1949 sheet: -1.83 (0.19), residues: 636 loop : -2.39 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 140 HIS 0.011 0.002 HIS N 287 PHE 0.021 0.002 PHE P 142 TYR 0.039 0.002 TYR B 348 ARG 0.013 0.001 ARG A1286 *********************** 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 673 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 673 time to evaluate : 5.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7435 (t0) cc_final: 0.6795 (t0) REVERT: A 138 MET cc_start: 0.8651 (mtm) cc_final: 0.8355 (mtp) REVERT: A 161 ASN cc_start: 0.8569 (m-40) cc_final: 0.8102 (t0) REVERT: A 188 LYS cc_start: 0.7721 (tppt) cc_final: 0.7482 (tppt) REVERT: A 273 MET cc_start: 0.5762 (mtp) cc_final: 0.5029 (ttm) REVERT: A 697 MET cc_start: 0.9413 (tmm) cc_final: 0.9066 (tmm) REVERT: A 863 PHE cc_start: 0.8709 (m-80) cc_final: 0.8406 (m-80) REVERT: A 921 LEU cc_start: 0.7868 (pt) cc_final: 0.7053 (pt) REVERT: A 922 ASP cc_start: 0.8189 (m-30) cc_final: 0.7678 (m-30) REVERT: A 960 MET cc_start: 0.8497 (mmt) cc_final: 0.8101 (mmm) REVERT: A 1028 MET cc_start: 0.7160 (mtp) cc_final: 0.6768 (mtt) REVERT: A 1343 MET cc_start: 0.8881 (mmt) cc_final: 0.7663 (mmm) REVERT: B 53 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8514 (mttm) REVERT: B 122 ASP cc_start: 0.8972 (m-30) cc_final: 0.8767 (m-30) REVERT: B 342 PHE cc_start: 0.8960 (m-10) cc_final: 0.8684 (m-80) REVERT: B 358 MET cc_start: 0.8923 (mtp) cc_final: 0.8467 (mtp) REVERT: B 364 LYS cc_start: 0.8870 (tptp) cc_final: 0.8624 (tppt) REVERT: B 445 LYS cc_start: 0.8650 (tttp) cc_final: 0.8314 (tppt) REVERT: B 449 MET cc_start: 0.7024 (mmm) cc_final: 0.6674 (mmm) REVERT: B 931 MET cc_start: 0.8620 (mpp) cc_final: 0.7858 (mpp) REVERT: B 953 MET cc_start: 0.8267 (mtt) cc_final: 0.7961 (mtt) REVERT: B 1119 MET cc_start: 0.8503 (mtm) cc_final: 0.7618 (mtp) REVERT: B 1145 ASP cc_start: 0.8266 (p0) cc_final: 0.7898 (p0) REVERT: C 32 ASN cc_start: 0.8603 (t0) cc_final: 0.8077 (t0) REVERT: D 152 GLU cc_start: 0.5662 (tm-30) cc_final: 0.5305 (tp30) REVERT: D 153 MET cc_start: 0.6363 (mtp) cc_final: 0.5939 (mtp) REVERT: E 22 MET cc_start: 0.9262 (tmm) cc_final: 0.8691 (tmm) REVERT: E 75 MET cc_start: 0.6650 (ppp) cc_final: 0.6139 (ppp) REVERT: E 95 THR cc_start: 0.8961 (p) cc_final: 0.8451 (p) REVERT: E 99 HIS cc_start: 0.8417 (m-70) cc_final: 0.8016 (m90) REVERT: E 104 ASN cc_start: 0.7880 (t0) cc_final: 0.7568 (t0) REVERT: F 85 MET cc_start: 0.8325 (tmm) cc_final: 0.8083 (tmm) REVERT: G 36 ASN cc_start: 0.7800 (t0) cc_final: 0.7313 (t0) REVERT: G 152 ARG cc_start: 0.6542 (mtm110) cc_final: 0.4912 (mpt90) REVERT: H 110 ASP cc_start: 0.8999 (p0) cc_final: 0.8516 (t0) REVERT: H 136 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8639 (ttmt) REVERT: H 138 GLU cc_start: 0.8599 (pm20) cc_final: 0.7976 (tp30) REVERT: I 11 MET cc_start: 0.8173 (tpp) cc_final: 0.7970 (tpt) REVERT: J 52 THR cc_start: 0.9360 (p) cc_final: 0.8748 (t) REVERT: K 110 GLU cc_start: 0.8645 (mp0) cc_final: 0.8040 (mp0) REVERT: K 129 ASP cc_start: 0.8582 (t70) cc_final: 0.8246 (t70) REVERT: M 165 ASP cc_start: 0.6603 (m-30) cc_final: 0.6109 (m-30) REVERT: M 166 MET cc_start: 0.7803 (mpp) cc_final: 0.7480 (mpp) REVERT: M 194 LYS cc_start: 0.7824 (tmtt) cc_final: 0.7267 (mptt) REVERT: N 398 SER cc_start: 0.8879 (m) cc_final: 0.8554 (t) REVERT: N 421 GLN cc_start: 0.6657 (pm20) cc_final: 0.6354 (pt0) REVERT: O 67 MET cc_start: 0.8802 (tpp) cc_final: 0.8570 (mmm) REVERT: O 105 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8579 (mtpt) REVERT: O 240 GLN cc_start: 0.8480 (mt0) cc_final: 0.7599 (tp40) REVERT: O 345 PHE cc_start: 0.8215 (m-80) cc_final: 0.7808 (m-80) REVERT: P 35 GLU cc_start: 0.6702 (pt0) cc_final: 0.6260 (tm-30) REVERT: P 68 ASP cc_start: 0.7441 (t0) cc_final: 0.7120 (t0) REVERT: P 102 ARG cc_start: 0.6555 (mmp-170) cc_final: 0.6161 (mmp80) REVERT: P 295 ASN cc_start: 0.8373 (m110) cc_final: 0.8082 (m-40) REVERT: P 311 TYR cc_start: 0.9011 (m-10) cc_final: 0.8642 (m-10) REVERT: U 111 THR cc_start: 0.7210 (t) cc_final: 0.5972 (t) REVERT: U 139 TYR cc_start: 0.7184 (m-10) cc_final: 0.6714 (m-10) REVERT: V 18 ASN cc_start: 0.8907 (t0) cc_final: 0.8359 (t0) REVERT: V 98 GLU cc_start: 0.8517 (pp20) cc_final: 0.8194 (pp20) REVERT: V 102 ASP cc_start: 0.8600 (p0) cc_final: 0.8255 (p0) REVERT: V 123 GLN cc_start: 0.9025 (pp30) cc_final: 0.8420 (pp30) REVERT: V 142 MET cc_start: 0.8827 (tmm) cc_final: 0.8420 (tmm) REVERT: V 169 HIS cc_start: 0.8209 (m90) cc_final: 0.7964 (m90) REVERT: V 257 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8533 (tm-30) REVERT: W 432 LEU cc_start: 0.7736 (pp) cc_final: 0.7479 (pp) REVERT: W 441 LEU cc_start: 0.8694 (pt) cc_final: 0.8323 (pt) REVERT: W 444 GLN cc_start: 0.8216 (mp10) cc_final: 0.7829 (mp10) REVERT: W 498 PHE cc_start: 0.6278 (m-80) cc_final: 0.5594 (m-80) outliers start: 0 outliers final: 0 residues processed: 673 average time/residue: 0.5498 time to fit residues: 633.0905 Evaluate side-chains 509 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 5.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 339 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 349 optimal weight: 7.9990 chunk 374 optimal weight: 3.9990 chunk 271 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 431 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN B 382 GLN B 596 GLN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN D 122 GLN D 125 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN H 139 ASN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 298 ASN ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 119 HIS ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 509 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 48905 Z= 0.246 Angle : 0.694 10.941 66567 Z= 0.354 Chirality : 0.046 0.359 7528 Planarity : 0.004 0.046 8090 Dihedral : 15.784 177.989 7646 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.18 % 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: -2.55 (0.11), residues: 5589 helix: -0.76 (0.12), residues: 1936 sheet: -1.77 (0.19), residues: 650 loop : -2.36 (0.11), residues: 3003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 140 HIS 0.019 0.002 HIS W 509 PHE 0.022 0.001 PHE N 307 TYR 0.025 0.002 TYR B 348 ARG 0.012 0.000 ARG A1380 *********************** 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 679 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 677 time to evaluate : 5.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7360 (t0) cc_final: 0.6708 (t0) REVERT: A 138 MET cc_start: 0.8646 (mtm) cc_final: 0.8357 (mtp) REVERT: A 142 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8587 (pttp) REVERT: A 161 ASN cc_start: 0.8586 (m-40) cc_final: 0.8094 (t0) REVERT: A 273 MET cc_start: 0.5747 (mtp) cc_final: 0.4955 (ttm) REVERT: A 325 MET cc_start: 0.8873 (tpp) cc_final: 0.8648 (tpp) REVERT: A 697 MET cc_start: 0.9414 (tmm) cc_final: 0.9188 (tmm) REVERT: A 960 MET cc_start: 0.8458 (mmt) cc_final: 0.8092 (mmm) REVERT: A 1028 MET cc_start: 0.7109 (mtp) cc_final: 0.6734 (mtt) REVERT: A 1343 MET cc_start: 0.8840 (mmt) cc_final: 0.7592 (mmm) REVERT: B 53 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8485 (mttm) REVERT: B 122 ASP cc_start: 0.8925 (m-30) cc_final: 0.8711 (m-30) REVERT: B 342 PHE cc_start: 0.8949 (m-10) cc_final: 0.8702 (m-80) REVERT: B 358 MET cc_start: 0.8924 (mtp) cc_final: 0.8458 (mtp) REVERT: B 364 LYS cc_start: 0.8848 (tptp) cc_final: 0.8615 (tppt) REVERT: B 382 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8138 (pp30) REVERT: B 445 LYS cc_start: 0.8654 (tttp) cc_final: 0.8328 (tppt) REVERT: B 449 MET cc_start: 0.7012 (mmm) cc_final: 0.6623 (mmm) REVERT: B 517 MET cc_start: 0.8999 (mmt) cc_final: 0.8673 (mmt) REVERT: B 567 PHE cc_start: 0.7949 (p90) cc_final: 0.7512 (p90) REVERT: B 591 TYR cc_start: 0.7767 (t80) cc_final: 0.7346 (t80) REVERT: B 931 MET cc_start: 0.8715 (mpp) cc_final: 0.8017 (mpp) REVERT: B 953 MET cc_start: 0.8272 (mtt) cc_final: 0.7992 (mtt) REVERT: B 1084 MET cc_start: 0.8515 (tpp) cc_final: 0.8068 (tpt) REVERT: B 1119 MET cc_start: 0.8530 (mtm) cc_final: 0.7596 (mtp) REVERT: B 1145 ASP cc_start: 0.8192 (p0) cc_final: 0.7836 (p0) REVERT: C 32 ASN cc_start: 0.8639 (t0) cc_final: 0.8155 (t0) REVERT: D 153 MET cc_start: 0.6523 (mtp) cc_final: 0.5819 (mtm) REVERT: E 22 MET cc_start: 0.9264 (tmm) cc_final: 0.8841 (tmm) REVERT: E 57 MET cc_start: 0.7315 (tpp) cc_final: 0.7030 (tpp) REVERT: E 75 MET cc_start: 0.6734 (ppp) cc_final: 0.6323 (ppp) REVERT: E 95 THR cc_start: 0.8948 (p) cc_final: 0.8431 (p) REVERT: E 99 HIS cc_start: 0.8412 (m-70) cc_final: 0.8052 (m90) REVERT: E 104 ASN cc_start: 0.8036 (t0) cc_final: 0.7739 (t0) REVERT: F 85 MET cc_start: 0.8256 (tmm) cc_final: 0.7795 (tmm) REVERT: F 151 LEU cc_start: 0.9306 (mm) cc_final: 0.9018 (mp) REVERT: G 36 ASN cc_start: 0.7787 (t0) cc_final: 0.7320 (t0) REVERT: G 152 ARG cc_start: 0.6626 (mtm110) cc_final: 0.5009 (mpt90) REVERT: H 97 MET cc_start: 0.9175 (mtm) cc_final: 0.8961 (mtm) REVERT: H 110 ASP cc_start: 0.8982 (p0) cc_final: 0.8484 (t0) REVERT: H 136 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8618 (ttmt) REVERT: H 138 GLU cc_start: 0.8587 (pm20) cc_final: 0.8068 (tp30) REVERT: I 11 MET cc_start: 0.8103 (tpp) cc_final: 0.7894 (tpt) REVERT: J 52 THR cc_start: 0.8891 (p) cc_final: 0.8591 (t) REVERT: K 110 GLU cc_start: 0.8655 (mp0) cc_final: 0.8019 (mp0) REVERT: M 165 ASP cc_start: 0.6635 (m-30) cc_final: 0.6165 (m-30) REVERT: M 166 MET cc_start: 0.7790 (mpp) cc_final: 0.7521 (mpp) REVERT: M 194 LYS cc_start: 0.7831 (tmtt) cc_final: 0.7277 (mptt) REVERT: M 200 ARG cc_start: 0.7414 (mmp80) cc_final: 0.6910 (ptm-80) REVERT: N 398 SER cc_start: 0.8856 (m) cc_final: 0.8571 (t) REVERT: O 67 MET cc_start: 0.8789 (tpp) cc_final: 0.8494 (mmm) REVERT: O 128 HIS cc_start: 0.9016 (m90) cc_final: 0.8331 (m90) REVERT: O 213 ASP cc_start: 0.8597 (p0) cc_final: 0.8174 (p0) REVERT: O 240 GLN cc_start: 0.8405 (mt0) cc_final: 0.7518 (tp40) REVERT: O 345 PHE cc_start: 0.8322 (m-80) cc_final: 0.7867 (m-80) REVERT: P 35 GLU cc_start: 0.6681 (pt0) cc_final: 0.6265 (tm-30) REVERT: P 68 ASP cc_start: 0.7341 (t0) cc_final: 0.7056 (t0) REVERT: P 102 ARG cc_start: 0.6402 (mmp-170) cc_final: 0.6090 (mmp80) REVERT: P 119 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6779 (t-90) REVERT: P 179 LEU cc_start: 0.8957 (tt) cc_final: 0.8574 (mt) REVERT: P 295 ASN cc_start: 0.8407 (m110) cc_final: 0.8145 (m-40) REVERT: P 311 TYR cc_start: 0.9036 (m-10) cc_final: 0.7956 (m-10) REVERT: U 111 THR cc_start: 0.6943 (t) cc_final: 0.6269 (t) REVERT: U 139 TYR cc_start: 0.7229 (m-10) cc_final: 0.6769 (m-80) REVERT: V 18 ASN cc_start: 0.8940 (t0) cc_final: 0.8383 (t0) REVERT: V 98 GLU cc_start: 0.8451 (pp20) cc_final: 0.8148 (pp20) REVERT: V 102 ASP cc_start: 0.8528 (p0) cc_final: 0.8202 (p0) REVERT: V 123 GLN cc_start: 0.9005 (pp30) cc_final: 0.8344 (pp30) REVERT: V 142 MET cc_start: 0.8822 (tmm) cc_final: 0.8441 (tmm) REVERT: V 257 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8519 (tm-30) REVERT: W 432 LEU cc_start: 0.7835 (pp) cc_final: 0.7607 (pp) REVERT: W 441 LEU cc_start: 0.8718 (pt) cc_final: 0.8339 (pt) REVERT: W 444 GLN cc_start: 0.8227 (mp10) cc_final: 0.7817 (mp10) REVERT: W 498 PHE cc_start: 0.6240 (m-80) cc_final: 0.5566 (m-80) outliers start: 2 outliers final: 0 residues processed: 679 average time/residue: 0.6048 time to fit residues: 706.6507 Evaluate side-chains 508 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 506 time to evaluate : 5.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 499 optimal weight: 9.9990 chunk 526 optimal weight: 0.9990 chunk 480 optimal weight: 7.9990 chunk 511 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 402 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 462 optimal weight: 8.9990 chunk 484 optimal weight: 8.9990 chunk 510 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN B 821 HIS B 883 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 509 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 48905 Z= 0.283 Angle : 0.711 11.205 66567 Z= 0.364 Chirality : 0.046 0.363 7528 Planarity : 0.004 0.064 8090 Dihedral : 15.789 177.839 7646 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -2.53 (0.11), residues: 5589 helix: -0.78 (0.12), residues: 1953 sheet: -1.75 (0.19), residues: 643 loop : -2.33 (0.11), residues: 2993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 140 HIS 0.028 0.002 HIS A 71 PHE 0.028 0.002 PHE B 567 TYR 0.025 0.002 TYR B 348 ARG 0.014 0.001 ARG V 149 *********************** 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 654 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 5.799 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 134 ASN cc_start: 0.7353 (t0) cc_final: 0.6708 (t0) REVERT: A 138 MET cc_start: 0.8627 (mtm) cc_final: 0.8424 (mtp) REVERT: A 142 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8584 (pttp) REVERT: A 161 ASN cc_start: 0.8649 (m-40) cc_final: 0.8163 (t0) REVERT: A 273 MET cc_start: 0.5895 (mtp) cc_final: 0.5120 (ttm) REVERT: A 665 ASP cc_start: 0.7811 (p0) cc_final: 0.7290 (t0) REVERT: A 697 MET cc_start: 0.9429 (tmm) cc_final: 0.9093 (tmm) REVERT: A 926 MET cc_start: 0.8806 (tpt) cc_final: 0.8601 (mmm) REVERT: A 960 MET cc_start: 0.8476 (mmt) cc_final: 0.8115 (mmm) REVERT: A 1028 MET cc_start: 0.7158 (mtp) cc_final: 0.6786 (mtt) REVERT: A 1343 MET cc_start: 0.8783 (mmt) cc_final: 0.7334 (mmm) REVERT: B 53 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8504 (mttm) REVERT: B 258 LYS cc_start: 0.9194 (mttm) cc_final: 0.8937 (mmtm) REVERT: B 358 MET cc_start: 0.8913 (mtp) cc_final: 0.8624 (mtp) REVERT: B 364 LYS cc_start: 0.8864 (tptp) cc_final: 0.8632 (tppt) REVERT: B 443 SER cc_start: 0.7770 (m) cc_final: 0.7445 (t) REVERT: B 445 LYS cc_start: 0.8673 (tttp) cc_final: 0.8342 (tppt) REVERT: B 449 MET cc_start: 0.7082 (mmm) cc_final: 0.6641 (mmm) REVERT: B 517 MET cc_start: 0.9080 (mmt) cc_final: 0.8561 (mmm) REVERT: B 591 TYR cc_start: 0.7783 (t80) cc_final: 0.7324 (t80) REVERT: B 931 MET cc_start: 0.8773 (mpp) cc_final: 0.8055 (mpp) REVERT: B 953 MET cc_start: 0.8288 (mtt) cc_final: 0.7985 (mtt) REVERT: B 1084 MET cc_start: 0.8799 (tpp) cc_final: 0.8319 (tpt) REVERT: B 1119 MET cc_start: 0.8501 (mtm) cc_final: 0.7539 (mtp) REVERT: B 1145 ASP cc_start: 0.8211 (p0) cc_final: 0.7834 (p0) REVERT: C 32 ASN cc_start: 0.8650 (t0) cc_final: 0.8066 (t0) REVERT: D 152 GLU cc_start: 0.5659 (tm-30) cc_final: 0.5348 (tp30) REVERT: D 153 MET cc_start: 0.6736 (mtp) cc_final: 0.5953 (mtm) REVERT: E 22 MET cc_start: 0.9273 (tmm) cc_final: 0.8662 (tmm) REVERT: E 57 MET cc_start: 0.7156 (tpp) cc_final: 0.6873 (tpp) REVERT: E 75 MET cc_start: 0.6848 (ppp) cc_final: 0.6268 (ppp) REVERT: E 95 THR cc_start: 0.8993 (p) cc_final: 0.8471 (p) REVERT: E 99 HIS cc_start: 0.8389 (m-70) cc_final: 0.8168 (m90) REVERT: E 104 ASN cc_start: 0.8083 (t0) cc_final: 0.7779 (t0) REVERT: F 85 MET cc_start: 0.8278 (tmm) cc_final: 0.7792 (tmm) REVERT: F 114 GLU cc_start: 0.8564 (pm20) cc_final: 0.8259 (pm20) REVERT: F 151 LEU cc_start: 0.9345 (mm) cc_final: 0.8985 (mp) REVERT: G 36 ASN cc_start: 0.7840 (t0) cc_final: 0.7346 (t0) REVERT: G 152 ARG cc_start: 0.6590 (mtm110) cc_final: 0.4913 (mpt90) REVERT: H 110 ASP cc_start: 0.9004 (p0) cc_final: 0.8498 (t0) REVERT: H 138 GLU cc_start: 0.8685 (pm20) cc_final: 0.8125 (tp30) REVERT: I 11 MET cc_start: 0.8155 (tpp) cc_final: 0.7946 (tpt) REVERT: K 110 GLU cc_start: 0.8660 (mp0) cc_final: 0.8028 (mp0) REVERT: L 38 LEU cc_start: 0.9056 (tp) cc_final: 0.8809 (tp) REVERT: M 165 ASP cc_start: 0.6730 (m-30) cc_final: 0.6215 (m-30) REVERT: M 166 MET cc_start: 0.7822 (mpp) cc_final: 0.7481 (mpp) REVERT: M 194 LYS cc_start: 0.7768 (tmtt) cc_final: 0.7188 (mptt) REVERT: O 67 MET cc_start: 0.8799 (tpp) cc_final: 0.8556 (mmm) REVERT: O 213 ASP cc_start: 0.8056 (p0) cc_final: 0.7841 (p0) REVERT: O 240 GLN cc_start: 0.8401 (mt0) cc_final: 0.7518 (tp40) REVERT: O 345 PHE cc_start: 0.8429 (m-80) cc_final: 0.8029 (m-80) REVERT: O 564 PHE cc_start: 0.8381 (m-80) cc_final: 0.8100 (m-80) REVERT: P 35 GLU cc_start: 0.6688 (pt0) cc_final: 0.6259 (tm-30) REVERT: P 68 ASP cc_start: 0.7405 (t0) cc_final: 0.7154 (t0) REVERT: P 102 ARG cc_start: 0.6243 (mmp-170) cc_final: 0.6013 (mmp-170) REVERT: P 179 LEU cc_start: 0.9010 (tt) cc_final: 0.8608 (mt) REVERT: P 295 ASN cc_start: 0.8489 (m110) cc_final: 0.8178 (m-40) REVERT: U 111 THR cc_start: 0.6899 (t) cc_final: 0.6065 (t) REVERT: U 139 TYR cc_start: 0.7018 (m-10) cc_final: 0.6497 (m-80) REVERT: V 18 ASN cc_start: 0.8908 (t0) cc_final: 0.8318 (t0) REVERT: V 98 GLU cc_start: 0.8496 (pp20) cc_final: 0.8240 (pp20) REVERT: V 123 GLN cc_start: 0.8946 (pp30) cc_final: 0.8404 (pp30) REVERT: V 142 MET cc_start: 0.8817 (tmm) cc_final: 0.8482 (tmm) REVERT: V 169 HIS cc_start: 0.8128 (m90) cc_final: 0.7897 (m90) REVERT: V 257 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8598 (tm-30) REVERT: W 300 LYS cc_start: 0.8172 (pttp) cc_final: 0.7686 (mtpt) REVERT: W 441 LEU cc_start: 0.8741 (pt) cc_final: 0.8343 (pt) REVERT: W 444 GLN cc_start: 0.8229 (mp10) cc_final: 0.7816 (mp10) REVERT: W 498 PHE cc_start: 0.6269 (m-80) cc_final: 0.5594 (m-80) REVERT: W 509 HIS cc_start: 0.9399 (m90) cc_final: 0.9187 (m-70) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.5677 time to fit residues: 635.7984 Evaluate side-chains 510 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 5.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 336 optimal weight: 0.0980 chunk 541 optimal weight: 6.9990 chunk 330 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 567 optimal weight: 10.0000 chunk 522 optimal weight: 8.9990 chunk 452 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 349 optimal weight: 8.9990 chunk 277 optimal weight: 2.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 ASN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 119 HIS ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 319 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 48905 Z= 0.249 Angle : 0.702 12.786 66567 Z= 0.358 Chirality : 0.046 0.325 7528 Planarity : 0.004 0.053 8090 Dihedral : 15.771 177.501 7646 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.04 % Allowed : 0.58 % Favored : 99.38 % 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: -2.46 (0.11), residues: 5589 helix: -0.69 (0.12), residues: 1956 sheet: -1.72 (0.19), residues: 654 loop : -2.31 (0.11), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 140 HIS 0.028 0.001 HIS A 71 PHE 0.029 0.002 PHE B 567 TYR 0.035 0.002 TYR B 348 ARG 0.008 0.000 ARG A1286 ********************** 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 668 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 666 time to evaluate : 6.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7300 (t0) cc_final: 0.6662 (t0) REVERT: A 142 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8598 (pttp) REVERT: A 161 ASN cc_start: 0.8584 (m-40) cc_final: 0.8185 (t0) REVERT: A 273 MET cc_start: 0.5871 (mtp) cc_final: 0.4996 (ttm) REVERT: A 665 ASP cc_start: 0.7855 (p0) cc_final: 0.7172 (t0) REVERT: A 697 MET cc_start: 0.9418 (tmm) cc_final: 0.9190 (tmm) REVERT: A 769 LEU cc_start: 0.7647 (tt) cc_final: 0.7445 (mt) REVERT: A 890 MET cc_start: 0.9091 (tpt) cc_final: 0.8726 (tpt) REVERT: A 926 MET cc_start: 0.8985 (tpt) cc_final: 0.8747 (mmm) REVERT: A 960 MET cc_start: 0.8436 (mmt) cc_final: 0.8073 (mmm) REVERT: A 1028 MET cc_start: 0.7138 (mtp) cc_final: 0.6766 (mtt) REVERT: A 1343 MET cc_start: 0.8821 (mmt) cc_final: 0.7429 (mmm) REVERT: B 53 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8489 (mmtp) REVERT: B 258 LYS cc_start: 0.9201 (mttm) cc_final: 0.8937 (mmtm) REVERT: B 294 ASP cc_start: 0.8323 (t0) cc_final: 0.8122 (t0) REVERT: B 358 MET cc_start: 0.8822 (mtp) cc_final: 0.8617 (mtp) REVERT: B 443 SER cc_start: 0.7792 (m) cc_final: 0.7495 (t) REVERT: B 445 LYS cc_start: 0.8670 (tttp) cc_final: 0.8325 (tppt) REVERT: B 449 MET cc_start: 0.7047 (mmm) cc_final: 0.6636 (mmm) REVERT: B 517 MET cc_start: 0.9043 (mmt) cc_final: 0.8503 (mmm) REVERT: B 591 TYR cc_start: 0.7786 (t80) cc_final: 0.7309 (t80) REVERT: B 670 MET cc_start: 0.7449 (mmt) cc_final: 0.7192 (mmm) REVERT: B 931 MET cc_start: 0.8788 (mpp) cc_final: 0.8080 (mpp) REVERT: B 953 MET cc_start: 0.8301 (mtt) cc_final: 0.8007 (mtt) REVERT: B 1068 ASP cc_start: 0.8173 (m-30) cc_final: 0.7917 (m-30) REVERT: B 1084 MET cc_start: 0.8733 (tpp) cc_final: 0.8309 (tpt) REVERT: B 1119 MET cc_start: 0.8484 (mtm) cc_final: 0.7578 (mtp) REVERT: B 1145 ASP cc_start: 0.8159 (p0) cc_final: 0.7786 (p0) REVERT: C 32 ASN cc_start: 0.8614 (t0) cc_final: 0.8057 (t0) REVERT: D 152 GLU cc_start: 0.5527 (tm-30) cc_final: 0.5213 (tp30) REVERT: D 153 MET cc_start: 0.6579 (mtp) cc_final: 0.6105 (mtm) REVERT: E 22 MET cc_start: 0.9283 (tmm) cc_final: 0.8797 (tmm) REVERT: E 57 MET cc_start: 0.7338 (tpp) cc_final: 0.7071 (tpp) REVERT: E 75 MET cc_start: 0.6862 (ppp) cc_final: 0.6271 (ppp) REVERT: E 93 MET cc_start: 0.8351 (mpp) cc_final: 0.8140 (mpp) REVERT: E 95 THR cc_start: 0.9017 (p) cc_final: 0.8486 (p) REVERT: E 99 HIS cc_start: 0.8365 (m-70) cc_final: 0.8124 (m90) REVERT: E 104 ASN cc_start: 0.7993 (t0) cc_final: 0.7677 (t0) REVERT: F 85 MET cc_start: 0.8254 (tmm) cc_final: 0.7768 (tmm) REVERT: F 114 GLU cc_start: 0.8557 (pm20) cc_final: 0.8334 (pm20) REVERT: F 151 LEU cc_start: 0.9328 (mm) cc_final: 0.8966 (mp) REVERT: G 36 ASN cc_start: 0.7814 (t0) cc_final: 0.7563 (t0) REVERT: G 152 ARG cc_start: 0.6609 (mtm110) cc_final: 0.4920 (mpt90) REVERT: H 110 ASP cc_start: 0.9003 (p0) cc_final: 0.8487 (t0) REVERT: H 138 GLU cc_start: 0.8672 (pm20) cc_final: 0.8074 (tp30) REVERT: I 11 MET cc_start: 0.8158 (tpp) cc_final: 0.7927 (tpt) REVERT: J 52 THR cc_start: 0.9430 (p) cc_final: 0.8576 (p) REVERT: K 110 GLU cc_start: 0.8656 (mp0) cc_final: 0.8013 (mp0) REVERT: M 165 ASP cc_start: 0.6686 (m-30) cc_final: 0.6223 (m-30) REVERT: M 166 MET cc_start: 0.7821 (mpp) cc_final: 0.7527 (mpp) REVERT: M 194 LYS cc_start: 0.7794 (tmtt) cc_final: 0.7197 (mptt) REVERT: M 200 ARG cc_start: 0.7227 (mmp80) cc_final: 0.6898 (ptm-80) REVERT: O 240 GLN cc_start: 0.8276 (mt0) cc_final: 0.7388 (tp40) REVERT: O 345 PHE cc_start: 0.8443 (m-80) cc_final: 0.8085 (m-80) REVERT: O 564 PHE cc_start: 0.8381 (m-80) cc_final: 0.8094 (m-80) REVERT: P 19 HIS cc_start: 0.8739 (p-80) cc_final: 0.8386 (p90) REVERT: P 35 GLU cc_start: 0.6676 (pt0) cc_final: 0.6261 (tm-30) REVERT: P 119 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6608 (t70) REVERT: P 179 LEU cc_start: 0.8988 (tt) cc_final: 0.8590 (mt) REVERT: P 295 ASN cc_start: 0.8421 (m110) cc_final: 0.8149 (m-40) REVERT: P 311 TYR cc_start: 0.8984 (m-10) cc_final: 0.8741 (m-10) REVERT: U 111 THR cc_start: 0.6894 (t) cc_final: 0.6073 (t) REVERT: U 139 TYR cc_start: 0.7062 (m-10) cc_final: 0.6489 (m-80) REVERT: V 18 ASN cc_start: 0.8895 (t0) cc_final: 0.8301 (t0) REVERT: V 123 GLN cc_start: 0.8859 (pp30) cc_final: 0.8499 (pp30) REVERT: V 169 HIS cc_start: 0.8217 (m90) cc_final: 0.7966 (m90) REVERT: V 257 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8553 (tm-30) REVERT: V 294 ARG cc_start: 0.6526 (mmt180) cc_final: 0.6181 (mmp80) REVERT: W 300 LYS cc_start: 0.8174 (pttp) cc_final: 0.7629 (mtpt) REVERT: W 441 LEU cc_start: 0.8711 (pt) cc_final: 0.8303 (pt) REVERT: W 444 GLN cc_start: 0.8292 (mp10) cc_final: 0.7837 (mp10) REVERT: W 498 PHE cc_start: 0.6210 (m-80) cc_final: 0.5561 (m-80) outliers start: 2 outliers final: 0 residues processed: 667 average time/residue: 0.5522 time to fit residues: 632.6014 Evaluate side-chains 516 residues out of total 5012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 515 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 359 optimal weight: 2.9990 chunk 481 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 416 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 chunk 452 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 465 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN C 175 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 319 GLN W 509 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.072942 restraints weight = 163913.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.074211 restraints weight = 106046.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074571 restraints weight = 71783.218| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 48905 Z= 0.213 Angle : 0.686 11.468 66567 Z= 0.347 Chirality : 0.045 0.348 7528 Planarity : 0.004 0.047 8090 Dihedral : 15.702 177.412 7646 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -2.38 (0.11), residues: 5589 helix: -0.61 (0.12), residues: 1961 sheet: -1.71 (0.19), residues: 651 loop : -2.28 (0.11), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 140 HIS 0.029 0.001 HIS A 71 PHE 0.029 0.001 PHE B 567 TYR 0.033 0.002 TYR V 92 ARG 0.008 0.000 ARG A1286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11739.01 seconds wall clock time: 213 minutes 30.27 seconds (12810.27 seconds total)