Starting phenix.real_space_refine on Mon Mar 25 13:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/03_2024/6eu0_3955_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/03_2024/6eu0_3955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/03_2024/6eu0_3955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/03_2024/6eu0_3955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/03_2024/6eu0_3955_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/03_2024/6eu0_3955_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 108 5.49 5 Mg 1 5.21 5 S 245 5.16 5 C 30570 2.51 5 N 8525 2.21 5 O 9462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ARG 1125": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "A ARG 1265": "NH1" <-> "NH2" Residue "A ARG 1337": "NH1" <-> "NH2" Residue "A ARG 1373": "NH1" <-> "NH2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 874": "NH1" <-> "NH2" Residue "B ARG 1038": "NH1" <-> "NH2" Residue "B ARG 1043": "NH1" <-> "NH2" Residue "B ARG 1056": "NH1" <-> "NH2" Residue "B ARG 1061": "NH1" <-> "NH2" Residue "B ARG 1082": "NH1" <-> "NH2" Residue "B ARG 1142": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "E ARG 7": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 12": "NH1" <-> "NH2" Residue "G ARG 147": "NH1" <-> "NH2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 199": "NH1" <-> "NH2" Residue "M ARG 208": "NH1" <-> "NH2" Residue "N ARG 292": "NH1" <-> "NH2" Residue "N ARG 303": "NH1" <-> "NH2" Residue "N ARG 364": "NH1" <-> "NH2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "O ARG 291": "NH1" <-> "NH2" Residue "O ARG 292": "NH1" <-> "NH2" Residue "O ARG 303": "NH1" <-> "NH2" Residue "O ARG 317": "NH1" <-> "NH2" Residue "O ARG 368": "NH1" <-> "NH2" Residue "O ARG 512": "NH1" <-> "NH2" Residue "O ARG 542": "NH1" <-> "NH2" Residue "O ARG 553": "NH1" <-> "NH2" Residue "O ARG 561": "NH1" <-> "NH2" Residue "O ARG 578": "NH1" <-> "NH2" Residue "P ARG 113": "NH1" <-> "NH2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "P TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 262": "NH1" <-> "NH2" Residue "V ARG 307": "NH1" <-> "NH2" Residue "V ARG 311": "NH1" <-> "NH2" Residue "V ARG 318": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "Y ARG 105": "NH1" <-> "NH2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ARG 121": "NH1" <-> "NH2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z ARG 276": "NH1" <-> "NH2" Residue "Z ARG 286": "NH1" <-> "NH2" Residue "Z PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 298": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48918 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 11119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 11119 Classifications: {'peptide': 1421} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 1356} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8771 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 43, 'TRANS': 1068} 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: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} 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: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1698 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 197} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1161 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 313 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} 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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, '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: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4421 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 531} Chain breaks: 1 Chain: "P" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2355 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 287} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "Q" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 589 Classifications: {'peptide': 88} Incomplete info: {'backbone_only': 24} Link IDs: {'PTRANS': 6, 'TRANS': 81} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1038 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1174 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "V" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 1829 Classifications: {'peptide': 273} Incomplete info: {'backbone_only': 107} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 234 Chain: "Y" 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: "Z" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2705 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: "Z" 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 565 SG CYS A 77 89.240 78.682 82.095 1.00 15.62 S ATOM 803 SG CYS A 107 70.622 120.519 94.308 1.00 25.60 S ATOM 826 SG CYS A 110 68.829 122.010 91.555 1.00 24.86 S ATOM 1192 SG CYS A 154 70.379 124.084 94.613 1.00 30.78 S ATOM 1216 SG CYS A 157 66.756 123.509 94.933 1.00 32.12 S ATOM 19552 SG CYS B1107 90.960 91.902 74.367 1.00 23.75 S ATOM 19572 SG CYS B1110 87.525 94.671 72.454 1.00 28.41 S ATOM 29029 SG CYS I 8 75.732 122.593 160.337 1.00 52.02 S ATOM 29157 SG CYS I 26 76.510 125.739 157.214 1.00 62.82 S ATOM 29180 SG CYS I 29 72.878 122.243 157.747 1.00 63.56 S ATOM 29338 SG CYS J 7 141.358 55.387 124.484 1.00 8.95 S ATOM 29641 SG CYS J 45 143.358 59.689 125.920 1.00 10.79 S ATOM 29647 SG CYS J 46 143.946 55.475 126.975 1.00 10.18 S ATOM 30831 SG CYS L 51 98.829 38.407 126.374 1.00 19.89 S ATOM 46256 SG CYS Z 7 104.254 57.406 75.138 1.00 58.99 S ATOM 46397 SG CYS Z 25 106.490 59.854 78.173 1.00 42.65 S ATOM 46417 SG CYS Z 28 108.589 59.174 75.011 1.00 38.35 S Time building chain proxies: 26.31, per 1000 atoms: 0.54 Number of scatterers: 48918 At special positions: 0 Unit cell: (198.22, 173.84, 205.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 245 16.00 P 108 15.00 Mg 1 11.99 O 9462 8.00 N 8525 7.00 C 30570 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: 18.66 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb=" ZN Z 601 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 7 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 28 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 25 " Number of angles added : 6 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11002 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 37.4% alpha, 7.1% beta 34 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 15.23 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.721A pdb=" N GLY A 59 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.980A pdb=" N LYS A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.984A pdb=" N LYS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP A 201 " --> pdb=" O TRP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.090A pdb=" N ARG A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.757A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 283 through 306 removed outlier: 3.596A pdb=" N SER A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 325 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.795A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.281A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.881A pdb=" N ALA A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 565 removed outlier: 3.632A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 605 through 615 removed outlier: 3.562A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 709 Proline residue: A 687 - end of helix removed outlier: 3.876A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 747 removed outlier: 3.602A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.965A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 810 Processing helix chain 'A' and resid 857 through 889 removed outlier: 4.022A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.633A pdb=" N ASP A 919 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 942 removed outlier: 4.224A pdb=" N ASP A 940 " --> pdb=" O ASN A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 968 removed outlier: 3.525A pdb=" N ILE A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 995 removed outlier: 3.754A pdb=" N VAL A 995 " --> pdb=" O ALA A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1027 removed outlier: 3.727A pdb=" N ARG A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1064 through 1081 removed outlier: 3.749A pdb=" N ARG A1068 " --> pdb=" O GLU A1064 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1098 Processing helix chain 'A' and resid 1122 through 1131 removed outlier: 3.614A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A1131 " --> pdb=" O LYS A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1161 removed outlier: 4.291A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1171 removed outlier: 4.015A pdb=" N PHE A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1210 removed outlier: 3.596A pdb=" N ALA A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1265 removed outlier: 3.527A pdb=" N LEU A1263 " --> pdb=" O ARG A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1270 removed outlier: 3.630A pdb=" N ASP A1269 " --> pdb=" O ALA A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1320 through 1345 removed outlier: 8.185A pdb=" N ILE A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N GLU A1329 " --> pdb=" O VAL A1325 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA A1330 " --> pdb=" O LEU A1326 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A1331 " --> pdb=" O GLY A1327 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A1339 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1361 removed outlier: 3.934A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1394 through 1402 removed outlier: 3.658A pdb=" N TYR A1402 " --> pdb=" O ASP A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1418 removed outlier: 3.956A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 3.798A pdb=" N SER A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A1428 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1455 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.801A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.130A pdb=" N LYS B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.944A pdb=" N GLN B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.506A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 removed outlier: 4.160A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 343 through 359 removed outlier: 3.508A pdb=" N ARG B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 379 through 407 removed outlier: 3.927A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.886A pdb=" N LEU B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.899A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 526 through 536 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.790A pdb=" N LEU B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS B 550 " --> pdb=" O ALA B 547 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 551' Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.545A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 633 removed outlier: 3.810A pdb=" N GLY B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 662 through 666 removed outlier: 4.029A pdb=" N ASP B 665 " --> pdb=" O TYR B 662 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 666' Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.807A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 680' Processing helix chain 'B' and resid 690 through 694 removed outlier: 3.584A pdb=" N HIS B 693 " --> pdb=" O TYR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 955 through 971 removed outlier: 4.188A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 995 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1066 through 1074 removed outlier: 4.168A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1082 Processing helix chain 'B' and resid 1122 through 1134 removed outlier: 3.654A pdb=" N LYS B1126 " --> pdb=" O PRO B1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.717A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET C 71 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.738A pdb=" N VAL C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 176 through 181 removed outlier: 4.083A pdb=" N ASP C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 4.231A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.613A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.704A pdb=" N LYS D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 48 removed outlier: 3.948A pdb=" N ARG D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 68 removed outlier: 4.238A pdb=" N ASN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 4.022A pdb=" N GLU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'E' and resid 2 through 27 removed outlier: 3.788A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.642A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 120 through 124 removed outlier: 4.385A pdb=" N LEU E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E 124 " --> pdb=" O MET E 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 120 through 124' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.527A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.573A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.947A pdb=" N THR G 27 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 174 removed outlier: 4.131A pdb=" N LEU G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.596A pdb=" N LEU J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 40 removed outlier: 4.334A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 72 through 82 removed outlier: 4.246A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.628A pdb=" N LEU K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 100 removed outlier: 3.845A pdb=" N LYS M 100 " --> pdb=" O VAL M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 136 removed outlier: 3.683A pdb=" N LYS M 135 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA M 136 " --> pdb=" O LYS M 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 132 through 136' Processing helix chain 'M' and resid 188 through 198 Processing helix chain 'M' and resid 205 through 209 Processing helix chain 'M' and resid 231 through 236 Processing helix chain 'M' and resid 252 through 266 removed outlier: 3.786A pdb=" N ASP M 257 " --> pdb=" O GLU M 253 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE M 259 " --> pdb=" O PHE M 255 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU M 262 " --> pdb=" O THR M 258 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA M 263 " --> pdb=" O ILE M 259 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU M 264 " --> pdb=" O VAL M 260 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS M 266 " --> pdb=" O GLU M 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 295 removed outlier: 3.715A pdb=" N LYS N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 57 removed outlier: 3.793A pdb=" N ALA O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 72 removed outlier: 3.953A pdb=" N ALA O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 83 removed outlier: 3.905A pdb=" N LEU O 79 " --> pdb=" O SER O 75 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 99 removed outlier: 3.959A pdb=" N THR O 93 " --> pdb=" O ASP O 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 138 removed outlier: 6.305A pdb=" N GLY O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 144 removed outlier: 4.069A pdb=" N GLN O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 165 removed outlier: 3.916A pdb=" N ALA O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN O 162 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL O 163 " --> pdb=" O ILE O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 175 Processing helix chain 'O' and resid 176 through 178 No H-bonds generated for 'chain 'O' and resid 176 through 178' Processing helix chain 'O' and resid 181 through 197 removed outlier: 4.337A pdb=" N TYR O 185 " --> pdb=" O ASP O 181 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR O 186 " --> pdb=" O SER O 182 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.750A pdb=" N ASN O 225 " --> pdb=" O LYS O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 255 Processing helix chain 'O' and resid 285 through 303 Processing helix chain 'O' and resid 306 through 320 removed outlier: 4.562A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) Processing helix chain 'O' and resid 339 through 356 removed outlier: 3.839A pdb=" N LYS O 343 " --> pdb=" O LEU O 339 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN O 346 " --> pdb=" O ALA O 342 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU O 353 " --> pdb=" O ALA O 349 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 367 Processing helix chain 'O' and resid 451 through 463 removed outlier: 3.505A pdb=" N SER O 455 " --> pdb=" O SER O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 500 removed outlier: 4.022A pdb=" N LEU O 500 " --> pdb=" O ILE O 496 " (cutoff:3.500A) Processing helix chain 'O' and resid 502 through 514 Processing helix chain 'O' and resid 519 through 524 removed outlier: 3.720A pdb=" N ASN O 523 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing helix chain 'O' and resid 530 through 542 Processing helix chain 'O' and resid 569 through 598 removed outlier: 3.710A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 610 removed outlier: 3.892A pdb=" N LEU O 603 " --> pdb=" O ASN O 599 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA O 606 " --> pdb=" O LEU O 602 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP O 609 " --> pdb=" O LYS O 605 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP O 610 " --> pdb=" O ALA O 606 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 651 removed outlier: 3.559A pdb=" N ASN O 625 " --> pdb=" O PRO O 621 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG O 643 " --> pdb=" O ALA O 639 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 24 Processing helix chain 'P' and resid 29 through 40 removed outlier: 3.911A pdb=" N GLN P 33 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 54 Processing helix chain 'P' and resid 89 through 99 removed outlier: 3.936A pdb=" N ALA P 99 " --> pdb=" O SER P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 113 removed outlier: 3.605A pdb=" N ILE P 110 " --> pdb=" O TRP P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 116 No H-bonds generated for 'chain 'P' and resid 114 through 116' Processing helix chain 'P' and resid 118 through 130 Processing helix chain 'P' and resid 172 through 190 Processing helix chain 'P' and resid 203 through 209 removed outlier: 3.999A pdb=" N PHE P 207 " --> pdb=" O LYS P 203 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR P 208 " --> pdb=" O LYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 228 removed outlier: 3.792A pdb=" N ALA P 228 " --> pdb=" O PHE P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 250 removed outlier: 3.619A pdb=" N ASP P 250 " --> pdb=" O VAL P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 273 Processing helix chain 'Q' and resid 48 through 67 removed outlier: 3.529A pdb=" N ARG Q 52 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 Processing helix chain 'Q' and resid 86 through 91 Processing helix chain 'Q' and resid 101 through 116 Processing helix chain 'V' and resid 293 through 317 removed outlier: 4.304A pdb=" N ALA V 299 " --> pdb=" O LYS V 295 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS V 300 " --> pdb=" O SER V 296 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS V 301 " --> pdb=" O LYS V 297 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA V 302 " --> pdb=" O MET V 298 " (cutoff:3.500A) Processing helix chain 'V' and resid 322 through 346 removed outlier: 3.610A pdb=" N LEU V 346 " --> pdb=" O GLU V 342 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 386 Processing helix chain 'V' and resid 421 through 435 Processing helix chain 'V' and resid 438 through 446 Processing helix chain 'V' and resid 450 through 465 removed outlier: 3.852A pdb=" N VAL V 454 " --> pdb=" O SER V 450 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS V 464 " --> pdb=" O ASN V 460 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG V 465 " --> pdb=" O GLU V 461 " (cutoff:3.500A) Processing helix chain 'V' and resid 466 through 476 removed outlier: 4.041A pdb=" N LYS V 476 " --> pdb=" O ALA V 472 " (cutoff:3.500A) Processing helix chain 'V' and resid 480 through 489 Processing helix chain 'V' and resid 496 through 541 removed outlier: 3.713A pdb=" N LYS V 541 " --> pdb=" O ASN V 537 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 89 removed outlier: 3.556A pdb=" N ALA Y 89 " --> pdb=" O ALA Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 147 removed outlier: 3.923A pdb=" N ALA Y 140 " --> pdb=" O SER Y 136 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG Y 141 " --> pdb=" O ARG Y 137 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE Y 142 " --> pdb=" O LYS Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 178 Processing helix chain 'Y' and resid 219 through 229 removed outlier: 3.570A pdb=" N ALA Y 229 " --> pdb=" O GLN Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 230 through 237 removed outlier: 3.619A pdb=" N PHE Y 237 " --> pdb=" O VAL Y 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 95 Processing helix chain 'Z' and resid 97 through 114 removed outlier: 3.784A pdb=" N THR Z 101 " --> pdb=" O PRO Z 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP Z 102 " --> pdb=" O GLU Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 122 through 137 removed outlier: 4.068A pdb=" N GLU Z 137 " --> pdb=" O ALA Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 148 removed outlier: 4.020A pdb=" N PHE Z 146 " --> pdb=" O MET Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 152 removed outlier: 3.866A pdb=" N VAL Z 152 " --> pdb=" O ARG Z 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 149 through 152' Processing helix chain 'Z' and resid 153 through 162 removed outlier: 3.599A pdb=" N ILE Z 157 " --> pdb=" O SER Z 153 " (cutoff:3.500A) Processing helix chain 'Z' and resid 179 through 186 removed outlier: 3.533A pdb=" N GLN Z 183 " --> pdb=" O SER Z 179 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA Z 186 " --> pdb=" O ILE Z 182 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 211 removed outlier: 3.851A pdb=" N ASP Z 201 " --> pdb=" O LYS Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 235 removed outlier: 5.206A pdb=" N ALA Z 231 " --> pdb=" O CYS Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 240 through 248 removed outlier: 3.898A pdb=" N ILE Z 244 " --> pdb=" O THR Z 240 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL Z 245 " --> pdb=" O HIS Z 241 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL Z 247 " --> pdb=" O GLU Z 243 " (cutoff:3.500A) Processing helix chain 'Z' and resid 251 through 266 removed outlier: 3.940A pdb=" N LEU Z 255 " --> pdb=" O ALA Z 251 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Z 256 " --> pdb=" O GLU Z 252 " (cutoff:3.500A) Processing helix chain 'Z' and resid 269 through 274 removed outlier: 4.568A pdb=" N GLN Z 273 " --> pdb=" O LYS Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 296 removed outlier: 3.843A pdb=" N VAL Z 291 " --> pdb=" O PRO Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 455 removed outlier: 4.040A pdb=" N LEU Z 452 " --> pdb=" O THR Z 448 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL Z 455 " --> pdb=" O TYR Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 480 through 491 Processing helix chain 'Z' and resid 492 through 509 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 16 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.594A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B1062 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 373 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.591A pdb=" N GLY A 377 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.677A pdb=" N VAL A 462 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 625 through 629 removed outlier: 6.845A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 897 through 898 Processing sheet with id=AA9, first strand: chain 'A' and resid 1281 through 1282 removed outlier: 3.647A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1173 through 1175 removed outlier: 3.502A pdb=" N GLN A1174 " --> pdb=" O GLN A1185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1224 through 1225 removed outlier: 3.543A pdb=" N ILE A1225 " --> pdb=" O ARG A1229 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A1229 " --> pdb=" O ILE A1225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1431 through 1432 removed outlier: 3.619A pdb=" N LYS A1432 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY G 57 " --> pdb=" O LYS A1432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 95 through 100 removed outlier: 6.791A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AB6, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.739A pdb=" N ARG B 376 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 199 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 561 through 564 removed outlier: 3.793A pdb=" N GLY B 563 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 613 through 614 Processing sheet with id=AB9, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.539A pdb=" N LEU B 899 " --> pdb=" O GLN B 883 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.539A pdb=" N LEU B 899 " --> pdb=" O GLN B 883 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 753 through 758 Processing sheet with id=AC3, first strand: chain 'B' and resid 753 through 758 Processing sheet with id=AC4, first strand: chain 'B' and resid 770 through 774 removed outlier: 7.688A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.494A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 871 " --> pdb=" O ILE B 843 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 1093 through 1094 Processing sheet with id=AC7, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AC8, first strand: chain 'C' and resid 44 through 47 removed outlier: 4.631A pdb=" N SER C 46 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 77 through 86 removed outlier: 5.121A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.768A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AD3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AD4, first strand: chain 'E' and resid 80 through 82 removed outlier: 6.578A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU E 133 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AD6, first strand: chain 'F' and resid 133 through 135 Processing sheet with id=AD7, first strand: chain 'G' and resid 5 through 13 removed outlier: 3.796A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL G 75 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR G 47 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 84 through 88 removed outlier: 3.946A pdb=" N VAL G 85 " --> pdb=" O PHE G 148 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 128 through 129 removed outlier: 4.620A pdb=" N TRP G 128 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE G 140 " --> pdb=" O TRP G 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'H' and resid 38 through 43 removed outlier: 8.182A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN H 11 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 57 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 104 through 106 removed outlier: 3.874A pdb=" N GLU H 105 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY H 127 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET H 123 " --> pdb=" O TYR H 116 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 23 through 24 removed outlier: 3.708A pdb=" N LEU I 24 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE I 33 " --> pdb=" O LEU I 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'K' and resid 60 through 66 removed outlier: 3.554A pdb=" N ALA K 61 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE K 105 " --> pdb=" O ALA K 61 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY K 90 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 88 through 89 removed outlier: 3.754A pdb=" N VAL N 394 " --> pdb=" O PHE M 88 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 109 through 111 removed outlier: 3.628A pdb=" N GLU M 120 " --> pdb=" O ARG M 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 158 through 159 Processing sheet with id=AE8, first strand: chain 'O' and resid 104 through 108 removed outlier: 3.930A pdb=" N LYS O 105 " --> pdb=" O TYR O 121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 549 through 550 removed outlier: 3.748A pdb=" N LEU O 565 " --> pdb=" O GLN O 549 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 66 through 75 removed outlier: 4.686A pdb=" N LEU Y 67 " --> pdb=" O VAL Y 161 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL Y 161 " --> pdb=" O LEU Y 67 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN Y 69 " --> pdb=" O ASN Y 159 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN Y 159 " --> pdb=" O ASN Y 69 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL Y 71 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE Y 157 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR Y 73 " --> pdb=" O PHE Y 155 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE Y 155 " --> pdb=" O THR Y 73 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE Y 160 " --> pdb=" O GLY Y 216 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY Y 216 " --> pdb=" O ILE Y 160 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 193 through 197 removed outlier: 3.536A pdb=" N ILE Y 202 " --> pdb=" O MET Y 197 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 13 through 14 removed outlier: 3.589A pdb=" N VAL Z 24 " --> pdb=" O GLU Z 13 " (cutoff:3.500A) 1465 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 19.56 Time building geometry restraints manager: 20.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13106 1.33 - 1.46: 9600 1.46 - 1.58: 26678 1.58 - 1.70: 212 1.70 - 1.82: 399 Bond restraints: 49995 Sorted by residual: bond pdb=" C ASP M 221 " pdb=" N PRO M 222 " ideal model delta sigma weight residual 1.334 1.409 -0.075 2.34e-02 1.83e+03 1.02e+01 bond pdb=" C LEU A1267 " pdb=" N PRO A1268 " ideal model delta sigma weight residual 1.339 1.436 -0.097 3.40e-02 8.65e+02 8.09e+00 bond pdb=" C4' DC S 30 " pdb=" O4' DC S 30 " ideal model delta sigma weight residual 1.450 1.399 0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C PHE B 949 " pdb=" N PRO B 950 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.70e+00 bond pdb=" C GLN P 154 " pdb=" N PRO P 155 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.36e+00 ... (remaining 49990 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.47: 1158 104.47 - 112.03: 22783 112.03 - 119.58: 19122 119.58 - 127.13: 24092 127.13 - 134.69: 721 Bond angle restraints: 67876 Sorted by residual: angle pdb=" N PRO B 817 " pdb=" CA PRO B 817 " pdb=" C PRO B 817 " ideal model delta sigma weight residual 111.33 119.80 -8.47 1.43e+00 4.89e-01 3.51e+01 angle pdb=" C GLY O 305 " pdb=" N SER O 306 " pdb=" CA SER O 306 " ideal model delta sigma weight residual 121.54 132.70 -11.16 1.91e+00 2.74e-01 3.41e+01 angle pdb=" C SER B 585 " pdb=" N GLU B 586 " pdb=" CA GLU B 586 " ideal model delta sigma weight residual 121.54 132.10 -10.56 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C LYS A 2 " pdb=" N GLU A 3 " pdb=" CA GLU A 3 " ideal model delta sigma weight residual 122.46 130.12 -7.66 1.41e+00 5.03e-01 2.95e+01 angle pdb=" O3' DA S 32 " pdb=" C3' DA S 32 " pdb=" C2' DA S 32 " ideal model delta sigma weight residual 111.50 103.36 8.14 1.50e+00 4.44e-01 2.95e+01 ... (remaining 67871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 29541 35.98 - 71.96: 712 71.96 - 107.93: 29 107.93 - 143.91: 2 143.91 - 179.89: 4 Dihedral angle restraints: 30288 sinusoidal: 13173 harmonic: 17115 Sorted by residual: dihedral pdb=" CA PHE P 300 " pdb=" C PHE P 300 " pdb=" N PRO P 301 " pdb=" CA PRO P 301 " ideal model delta harmonic sigma weight residual 180.00 115.73 64.27 0 5.00e+00 4.00e-02 1.65e+02 dihedral pdb=" CA PHE M 130 " pdb=" C PHE M 130 " pdb=" N TYR M 131 " pdb=" CA TYR M 131 " ideal model delta harmonic sigma weight residual -180.00 -130.39 -49.61 0 5.00e+00 4.00e-02 9.84e+01 dihedral pdb=" CA PRO A 600 " pdb=" C PRO A 600 " pdb=" N TYR A 601 " pdb=" CA TYR A 601 " ideal model delta harmonic sigma weight residual -180.00 -135.78 -44.22 0 5.00e+00 4.00e-02 7.82e+01 ... (remaining 30285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 6334 0.075 - 0.151: 1086 0.151 - 0.226: 138 0.226 - 0.301: 20 0.301 - 0.376: 2 Chirality restraints: 7580 Sorted by residual: chirality pdb=" CG LEU D 28 " pdb=" CB LEU D 28 " pdb=" CD1 LEU D 28 " pdb=" CD2 LEU D 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE Q 79 " pdb=" CA ILE Q 79 " pdb=" CG1 ILE Q 79 " pdb=" CG2 ILE Q 79 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A 234 " pdb=" CA ILE A 234 " pdb=" CG1 ILE A 234 " pdb=" CG2 ILE A 234 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 7577 not shown) Planarity restraints: 8407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU Z 506 " 0.026 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C GLU Z 506 " -0.086 2.00e-02 2.50e+03 pdb=" O GLU Z 506 " 0.031 2.00e-02 2.50e+03 pdb=" N ALA Z 507 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE M 130 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C PHE M 130 " 0.083 2.00e-02 2.50e+03 pdb=" O PHE M 130 " -0.032 2.00e-02 2.50e+03 pdb=" N TYR M 131 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE P 300 " 0.071 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO P 301 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO P 301 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO P 301 " 0.059 5.00e-02 4.00e+02 ... (remaining 8404 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 197 2.48 - 3.09: 30456 3.09 - 3.69: 73818 3.69 - 4.30: 101116 4.30 - 4.90: 162804 Nonbonded interactions: 368391 Sorted by model distance: nonbonded pdb=" OD2 ASP A 511 " pdb="MG MG A2002 " model vdw 1.879 2.170 nonbonded pdb=" NZ LYS O 289 " pdb=" O PRO O 324 " model vdw 2.099 2.520 nonbonded pdb=" NH2 ARG B 576 " pdb=" OE1 GLU B 647 " model vdw 2.115 2.520 nonbonded pdb=" NZ LYS E 161 " pdb=" O GLY E 193 " model vdw 2.116 2.520 nonbonded pdb=" O ALA M 263 " pdb=" NZ LYS M 266 " model vdw 2.121 2.520 ... (remaining 368386 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: 1.690 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: 0.040 Extract box with map and model: 9.140 Check model and map are aligned: 0.690 Set scattering table: 0.400 Process input model: 140.550 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.190 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 : 0.005 0.097 49995 Z= 0.293 Angle : 1.075 15.478 67876 Z= 0.570 Chirality : 0.058 0.376 7580 Planarity : 0.007 0.110 8407 Dihedral : 14.423 179.888 19286 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.38 % Favored : 84.28 % Rotamer: Outliers : 0.53 % Allowed : 7.37 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 2.81 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.08), residues: 5885 helix: -3.02 (0.08), residues: 2067 sheet: -3.17 (0.23), residues: 394 loop : -4.04 (0.08), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 119 HIS 0.012 0.002 HIS A 92 PHE 0.037 0.002 PHE V 458 TYR 0.033 0.002 TYR O 132 ARG 0.010 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1751 time to evaluate : 5.543 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: A 57 LYS cc_start: 0.8365 (pttt) cc_final: 0.7983 (tptt) REVERT: A 126 GLU cc_start: 0.6118 (pm20) cc_final: 0.5858 (tm-30) REVERT: A 146 ASP cc_start: 0.6578 (p0) cc_final: 0.5997 (t70) REVERT: A 609 VAL cc_start: 0.9494 (t) cc_final: 0.9238 (t) REVERT: A 679 TYR cc_start: 0.8497 (t80) cc_final: 0.8221 (t80) REVERT: A 705 LEU cc_start: 0.7968 (tp) cc_final: 0.7567 (tp) REVERT: A 804 LEU cc_start: 0.8935 (tp) cc_final: 0.8695 (pp) REVERT: A 838 ASN cc_start: 0.7471 (m110) cc_final: 0.7031 (p0) REVERT: A 861 PHE cc_start: 0.8127 (t80) cc_final: 0.7823 (t80) REVERT: A 1051 ASN cc_start: 0.7414 (p0) cc_final: 0.6657 (t0) REVERT: A 1052 VAL cc_start: 0.8429 (t) cc_final: 0.7978 (m) REVERT: A 1128 GLU cc_start: 0.6979 (tt0) cc_final: 0.6298 (pt0) REVERT: A 1318 HIS cc_start: 0.5145 (m-70) cc_final: 0.4578 (m-70) REVERT: B 427 ASN cc_start: 0.7494 (t0) cc_final: 0.7286 (t0) REVERT: B 656 ASP cc_start: 0.6039 (t0) cc_final: 0.5702 (t0) REVERT: B 851 SER cc_start: 0.7273 (p) cc_final: 0.6698 (t) REVERT: B 1005 TYR cc_start: 0.7906 (m-10) cc_final: 0.7674 (m-10) REVERT: C 223 SER cc_start: 0.8617 (m) cc_final: 0.8240 (t) REVERT: D 117 LYS cc_start: 0.6766 (pmtt) cc_final: 0.6279 (pttt) REVERT: G 50 ASP cc_start: 0.8151 (p0) cc_final: 0.7270 (p0) REVERT: I 40 ILE cc_start: 0.2683 (tt) cc_final: 0.2431 (mm) REVERT: J 14 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7494 (t) REVERT: J 55 ASP cc_start: 0.7001 (t0) cc_final: 0.6712 (t0) REVERT: M 90 TYR cc_start: 0.7284 (m-10) cc_final: 0.6844 (m-10) REVERT: O 60 ARG cc_start: 0.5438 (ptp-170) cc_final: 0.4879 (mmt-90) REVERT: O 333 THR cc_start: 0.7622 (m) cc_final: 0.7359 (m) REVERT: O 565 LEU cc_start: 0.6926 (pt) cc_final: 0.6483 (mp) REVERT: O 577 MET cc_start: 0.7235 (mmm) cc_final: 0.6996 (tpp) REVERT: P 256 VAL cc_start: 0.6543 (t) cc_final: 0.6337 (t) REVERT: P 293 ILE cc_start: 0.5421 (mm) cc_final: 0.5212 (mm) REVERT: P 312 PHE cc_start: 0.3979 (t80) cc_final: 0.2856 (t80) REVERT: V 295 LYS cc_start: 0.6027 (mmtp) cc_final: 0.5736 (mmtp) REVERT: V 464 LYS cc_start: 0.4698 (OUTLIER) cc_final: 0.2904 (pttp) REVERT: Y 104 MET cc_start: 0.6350 (pmm) cc_final: 0.4029 (ttt) REVERT: Z 164 MET cc_start: 0.5584 (ppp) cc_final: 0.5369 (mmm) outliers start: 27 outliers final: 3 residues processed: 1769 average time/residue: 0.6762 time to fit residues: 1920.0421 Evaluate side-chains 887 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 882 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain V residue 464 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 504 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 348 optimal weight: 3.9990 chunk 542 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 161 ASN A 229 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN A 328 ASN A 333 ASN A 355 GLN A 427 HIS A 533 ASN A 913 GLN A1118 ASN A1180 ASN A1284 ASN A1317 ASN A1318 HIS A1354 HIS A1453 ASN B 42 GLN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 286 ASN B 362 ASN B 382 GLN ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 519 HIS B 574 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN B 859 ASN B 861 ASN ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 HIS B 928 GLN B 936 GLN B 947 HIS B 970 ASN B1077 GLN C 3 ASN C 65 ASN C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 69 ASN E 5 ASN E 63 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 28 HIS G 31 ASN G 173 GLN H 11 GLN H 35 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN M 167 GLN M 254 GLN N 289 HIS ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 GLN O 207 HIS ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 469 ASN ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 631 ASN P 19 HIS P 117 HIS P 119 HIS ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 305 HIS Q 60 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 319 GLN V 391 ASN ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 444 GLN ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 179 HIS Z 18 ASN Z 82 ASN Z 123 GLN Z 207 GLN Z 249 HIS Z 260 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 49995 Z= 0.352 Angle : 0.846 11.210 67876 Z= 0.437 Chirality : 0.049 0.350 7580 Planarity : 0.006 0.090 8407 Dihedral : 15.219 179.333 7657 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.34 % Favored : 84.44 % Rotamer: Outliers : 5.26 % Allowed : 16.21 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.80 % Twisted General : 0.26 % 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: -4.09 (0.09), residues: 5885 helix: -1.44 (0.10), residues: 2097 sheet: -2.76 (0.23), residues: 415 loop : -3.77 (0.09), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 316 HIS 0.010 0.002 HIS A 92 PHE 0.033 0.003 PHE V 439 TYR 0.033 0.002 TYR M 131 ARG 0.008 0.001 ARG B 788 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 949 time to evaluate : 5.261 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 17 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8346 (mm-30) REVERT: A 38 ASP cc_start: 0.6297 (m-30) cc_final: 0.5715 (m-30) REVERT: A 146 ASP cc_start: 0.6391 (p0) cc_final: 0.5942 (t70) REVERT: A 184 ARG cc_start: 0.6912 (tmt-80) cc_final: 0.6477 (tmt-80) REVERT: A 861 PHE cc_start: 0.8144 (t80) cc_final: 0.7881 (t80) REVERT: A 988 ASP cc_start: 0.7255 (p0) cc_final: 0.6702 (m-30) REVERT: A 1051 ASN cc_start: 0.7457 (p0) cc_final: 0.6923 (t0) REVERT: A 1052 VAL cc_start: 0.8470 (t) cc_final: 0.8007 (m) REVERT: A 1082 ARG cc_start: 0.8303 (ttm110) cc_final: 0.8103 (ttm110) REVERT: A 1128 GLU cc_start: 0.7344 (tt0) cc_final: 0.6960 (pt0) REVERT: A 1158 LYS cc_start: 0.6415 (tttp) cc_final: 0.6207 (tttt) REVERT: B 185 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7939 (p90) REVERT: B 325 GLU cc_start: 0.6036 (mp0) cc_final: 0.5295 (mp0) REVERT: B 365 MET cc_start: 0.6865 (ppp) cc_final: 0.6476 (ptt) REVERT: B 449 MET cc_start: 0.7347 (ppp) cc_final: 0.6896 (ppp) REVERT: B 851 SER cc_start: 0.7332 (p) cc_final: 0.6965 (t) REVERT: B 944 MET cc_start: 0.7701 (ttp) cc_final: 0.7328 (tmm) REVERT: B 1024 TYR cc_start: 0.7994 (m-80) cc_final: 0.7652 (m-10) REVERT: B 1052 GLU cc_start: 0.6656 (pp20) cc_final: 0.6127 (pp20) REVERT: B 1060 LEU cc_start: 0.7822 (mt) cc_final: 0.7528 (mt) REVERT: B 1136 ASN cc_start: 0.6337 (t0) cc_final: 0.6080 (t0) REVERT: C 131 THR cc_start: 0.7509 (m) cc_final: 0.7140 (p) REVERT: D 117 LYS cc_start: 0.6908 (pmtt) cc_final: 0.6656 (pttt) REVERT: D 153 MET cc_start: 0.6359 (mpp) cc_final: 0.5806 (mmt) REVERT: E 183 PRO cc_start: 0.9130 (Cg_endo) cc_final: 0.8849 (Cg_exo) REVERT: F 116 ASP cc_start: 0.8179 (t70) cc_final: 0.7945 (m-30) REVERT: G 50 ASP cc_start: 0.8229 (p0) cc_final: 0.7602 (p0) REVERT: G 170 GLU cc_start: 0.5379 (OUTLIER) cc_final: 0.4210 (tt0) REVERT: H 44 VAL cc_start: 0.8723 (p) cc_final: 0.8477 (t) REVERT: H 97 MET cc_start: 0.8920 (mmm) cc_final: 0.8678 (mmm) REVERT: I 40 ILE cc_start: 0.3615 (tt) cc_final: 0.2938 (mm) REVERT: J 55 ASP cc_start: 0.6915 (t0) cc_final: 0.6537 (t0) REVERT: K 142 MET cc_start: 0.5230 (ptm) cc_final: 0.4901 (ptp) REVERT: M 90 TYR cc_start: 0.7631 (m-10) cc_final: 0.7082 (m-10) REVERT: M 92 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6396 (t0) REVERT: M 159 TYR cc_start: 0.7145 (m-80) cc_final: 0.6927 (m-10) REVERT: M 162 PHE cc_start: 0.5594 (m-10) cc_final: 0.5345 (m-10) REVERT: M 163 VAL cc_start: 0.6313 (OUTLIER) cc_final: 0.6057 (p) REVERT: M 190 ASN cc_start: 0.6531 (OUTLIER) cc_final: 0.5912 (p0) REVERT: N 279 GLU cc_start: 0.7231 (tt0) cc_final: 0.6982 (tt0) REVERT: O 60 ARG cc_start: 0.5919 (ptp-170) cc_final: 0.4975 (mmt-90) REVERT: O 203 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7225 (pp) REVERT: O 282 ILE cc_start: 0.6861 (tp) cc_final: 0.6381 (tp) REVERT: O 368 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6985 (ttp80) REVERT: O 544 ASN cc_start: 0.8115 (t0) cc_final: 0.7703 (t0) REVERT: O 565 LEU cc_start: 0.7082 (pt) cc_final: 0.6644 (mp) REVERT: O 579 GLN cc_start: 0.7436 (pp30) cc_final: 0.7126 (pp30) REVERT: P 48 LEU cc_start: 0.5925 (mt) cc_final: 0.5538 (mt) REVERT: P 312 PHE cc_start: 0.4558 (t80) cc_final: 0.3255 (t80) REVERT: Q 58 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.3999 (t80) REVERT: Q 80 ASP cc_start: 0.7113 (m-30) cc_final: 0.6215 (m-30) REVERT: V 483 GLU cc_start: 0.4562 (OUTLIER) cc_final: 0.4321 (pt0) REVERT: Y 104 MET cc_start: 0.7057 (pmm) cc_final: 0.4140 (ttt) REVERT: Y 152 PHE cc_start: 0.2383 (t80) cc_final: 0.2093 (t80) REVERT: Z 164 MET cc_start: 0.6240 (ppp) cc_final: 0.5379 (mmp) REVERT: Z 235 ASN cc_start: 0.7148 (OUTLIER) cc_final: 0.6806 (t0) outliers start: 269 outliers final: 149 residues processed: 1131 average time/residue: 0.6256 time to fit residues: 1179.1459 Evaluate side-chains 921 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 762 time to evaluate : 5.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1342 THR Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1003 MET Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 200 CYS Chi-restraints excluded: chain G residue 210 TRP Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 219 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 226 THR Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 299 MET Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain V residue 487 GLU Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 124 ASN Chi-restraints excluded: chain Z residue 128 SER Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 145 ASP Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 245 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 301 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 451 optimal weight: 1.9990 chunk 369 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 543 optimal weight: 40.0000 chunk 586 optimal weight: 0.9990 chunk 483 optimal weight: 7.9990 chunk 538 optimal weight: 0.4980 chunk 185 optimal weight: 4.9990 chunk 435 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 540 ASN A 838 ASN A 843 GLN A1284 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 595 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 65 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN E 153 HIS ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 173 GLN ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 229 ASN O 257 ASN ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 49995 Z= 0.200 Angle : 0.730 12.300 67876 Z= 0.372 Chirality : 0.045 0.344 7580 Planarity : 0.005 0.086 8407 Dihedral : 14.984 175.643 7654 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.41 % Favored : 85.35 % Rotamer: Outliers : 4.77 % Allowed : 19.24 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.80 % Twisted General : 0.19 % 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: -3.54 (0.10), residues: 5885 helix: -0.80 (0.11), residues: 2117 sheet: -2.42 (0.24), residues: 413 loop : -3.59 (0.09), residues: 3355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 316 HIS 0.014 0.001 HIS B 144 PHE 0.034 0.002 PHE V 439 TYR 0.025 0.002 TYR M 131 ARG 0.006 0.001 ARG Z 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 887 time to evaluate : 5.608 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 1 MET cc_start: 0.5888 (ppp) cc_final: 0.5536 (ppp) REVERT: A 38 ASP cc_start: 0.5974 (m-30) cc_final: 0.5681 (m-30) REVERT: A 146 ASP cc_start: 0.6504 (p0) cc_final: 0.5884 (t70) REVERT: A 184 ARG cc_start: 0.6806 (tmt-80) cc_final: 0.6393 (tmt-80) REVERT: A 273 MET cc_start: 0.5490 (mmt) cc_final: 0.5272 (mmt) REVERT: A 320 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 481 HIS cc_start: 0.7630 (p-80) cc_final: 0.7374 (p90) REVERT: A 530 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 769 LEU cc_start: 0.8672 (mp) cc_final: 0.8406 (tp) REVERT: A 861 PHE cc_start: 0.8101 (t80) cc_final: 0.7867 (t80) REVERT: A 988 ASP cc_start: 0.7341 (p0) cc_final: 0.6777 (m-30) REVERT: A 1051 ASN cc_start: 0.7279 (p0) cc_final: 0.6852 (t0) REVERT: A 1052 VAL cc_start: 0.8478 (t) cc_final: 0.7963 (m) REVERT: A 1082 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8078 (ttm110) REVERT: A 1083 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7162 (tp) REVERT: A 1278 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 1394 ASP cc_start: 0.7275 (p0) cc_final: 0.7039 (p0) REVERT: B 96 VAL cc_start: 0.7202 (OUTLIER) cc_final: 0.6971 (t) REVERT: B 271 LEU cc_start: 0.6956 (tp) cc_final: 0.6510 (tp) REVERT: B 325 GLU cc_start: 0.5634 (mp0) cc_final: 0.5040 (mp0) REVERT: B 365 MET cc_start: 0.6818 (ppp) cc_final: 0.6420 (ptt) REVERT: B 409 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6286 (ptpp) REVERT: B 449 MET cc_start: 0.7345 (ppp) cc_final: 0.6497 (ppp) REVERT: B 652 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7459 (p0) REVERT: B 1024 TYR cc_start: 0.7864 (m-80) cc_final: 0.7628 (m-10) REVERT: B 1035 MET cc_start: 0.8761 (tpp) cc_final: 0.8114 (tpp) REVERT: B 1052 GLU cc_start: 0.6427 (pp20) cc_final: 0.5932 (pp20) REVERT: B 1060 LEU cc_start: 0.7786 (mt) cc_final: 0.7511 (mt) REVERT: B 1084 MET cc_start: 0.7665 (ttt) cc_final: 0.7200 (ttp) REVERT: B 1117 ILE cc_start: 0.8828 (pt) cc_final: 0.8363 (mp) REVERT: B 1131 GLU cc_start: 0.8080 (pt0) cc_final: 0.7708 (pp20) REVERT: C 3 ASN cc_start: 0.5987 (OUTLIER) cc_final: 0.5652 (m110) REVERT: C 131 THR cc_start: 0.7512 (m) cc_final: 0.6930 (p) REVERT: D 117 LYS cc_start: 0.6838 (pmtt) cc_final: 0.6471 (pttt) REVERT: D 153 MET cc_start: 0.6103 (mpp) cc_final: 0.5856 (mmt) REVERT: E 183 PRO cc_start: 0.9200 (Cg_endo) cc_final: 0.8985 (Cg_exo) REVERT: F 89 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7794 (mt-10) REVERT: F 116 ASP cc_start: 0.8410 (t70) cc_final: 0.7802 (m-30) REVERT: G 50 ASP cc_start: 0.7947 (p0) cc_final: 0.7302 (p0) REVERT: G 67 TYR cc_start: 0.7384 (m-80) cc_final: 0.6967 (m-80) REVERT: G 102 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5573 (tt) REVERT: G 170 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.3766 (tt0) REVERT: H 44 VAL cc_start: 0.8785 (p) cc_final: 0.8509 (t) REVERT: I 1 MET cc_start: 0.3603 (ttm) cc_final: 0.3360 (ttm) REVERT: I 40 ILE cc_start: 0.3306 (tt) cc_final: 0.2818 (mm) REVERT: J 55 ASP cc_start: 0.6703 (t0) cc_final: 0.6453 (t0) REVERT: K 44 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6625 (ttp-170) REVERT: K 91 TYR cc_start: 0.8255 (p90) cc_final: 0.8046 (p90) REVERT: M 90 TYR cc_start: 0.7725 (m-10) cc_final: 0.7314 (m-10) REVERT: M 163 VAL cc_start: 0.6003 (OUTLIER) cc_final: 0.5787 (t) REVERT: M 190 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.6385 (p0) REVERT: N 279 GLU cc_start: 0.7124 (tt0) cc_final: 0.6880 (tt0) REVERT: N 362 SER cc_start: 0.6405 (OUTLIER) cc_final: 0.5855 (t) REVERT: O 60 ARG cc_start: 0.6012 (ptp-170) cc_final: 0.5075 (mmt-90) REVERT: O 368 ARG cc_start: 0.7355 (mmm-85) cc_final: 0.7015 (ttp80) REVERT: O 565 LEU cc_start: 0.7155 (pt) cc_final: 0.6902 (mp) REVERT: P 146 LYS cc_start: 0.4159 (OUTLIER) cc_final: 0.3815 (mttt) REVERT: Q 80 ASP cc_start: 0.6832 (m-30) cc_final: 0.6522 (m-30) REVERT: V 464 LYS cc_start: 0.4771 (OUTLIER) cc_final: 0.3130 (pttp) REVERT: V 483 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.4129 (pt0) REVERT: Y 104 MET cc_start: 0.7051 (pmm) cc_final: 0.3906 (ttt) REVERT: Z 164 MET cc_start: 0.6214 (ppp) cc_final: 0.5316 (mmp) REVERT: Z 234 MET cc_start: 0.7405 (mtp) cc_final: 0.7169 (mtm) REVERT: Z 235 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6775 (t0) REVERT: Z 294 ARG cc_start: 0.7072 (ttp-110) cc_final: 0.6670 (tpt170) outliers start: 244 outliers final: 140 residues processed: 1045 average time/residue: 0.5631 time to fit residues: 995.5602 Evaluate side-chains 906 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 750 time to evaluate : 5.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1003 MET Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 210 TRP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 370 LEU Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain P residue 146 LYS Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain V residue 398 ASP Chi-restraints excluded: chain V residue 411 TYR Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain Z residue 182 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 250 VAL Chi-restraints excluded: chain Z residue 453 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 536 optimal weight: 0.9980 chunk 408 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 364 optimal weight: 7.9990 chunk 545 optimal weight: 20.0000 chunk 577 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 516 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1346 HIS ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS B 427 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 584 ASN P 197 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 ASN Z 35 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 49995 Z= 0.376 Angle : 0.823 13.029 67876 Z= 0.423 Chirality : 0.048 0.363 7580 Planarity : 0.006 0.081 8407 Dihedral : 15.126 172.595 7654 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 16.81 % Favored : 82.99 % Rotamer: Outliers : 6.47 % Allowed : 19.49 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.26 % 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: -3.40 (0.10), residues: 5885 helix: -0.61 (0.11), residues: 2094 sheet: -2.34 (0.25), residues: 403 loop : -3.54 (0.09), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 316 HIS 0.024 0.002 HIS B 144 PHE 0.041 0.002 PHE B 587 TYR 0.029 0.002 TYR M 131 ARG 0.010 0.001 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 803 time to evaluate : 5.625 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 17 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8339 (mm-30) REVERT: A 38 ASP cc_start: 0.6427 (m-30) cc_final: 0.6143 (m-30) REVERT: A 146 ASP cc_start: 0.6591 (p0) cc_final: 0.5992 (t70) REVERT: A 184 ARG cc_start: 0.7407 (tmt-80) cc_final: 0.6761 (tmt-80) REVERT: A 320 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 372 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7049 (mmm-85) REVERT: A 769 LEU cc_start: 0.8864 (mp) cc_final: 0.8473 (tp) REVERT: A 861 PHE cc_start: 0.8256 (t80) cc_final: 0.8029 (t80) REVERT: A 915 THR cc_start: 0.9256 (t) cc_final: 0.9031 (m) REVERT: A 1051 ASN cc_start: 0.7561 (p0) cc_final: 0.7221 (t0) REVERT: A 1052 VAL cc_start: 0.8520 (t) cc_final: 0.8217 (m) REVERT: A 1060 TYR cc_start: 0.7168 (m-80) cc_final: 0.6787 (m-80) REVERT: A 1082 ARG cc_start: 0.8338 (ttm110) cc_final: 0.8136 (ttm110) REVERT: A 1278 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8010 (mm) REVERT: A 1394 ASP cc_start: 0.7526 (p0) cc_final: 0.7296 (p0) REVERT: B 96 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.7031 (t) REVERT: B 185 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7407 (p90) REVERT: B 241 TYR cc_start: 0.6034 (m-80) cc_final: 0.4351 (m-80) REVERT: B 271 LEU cc_start: 0.7134 (tp) cc_final: 0.6558 (tp) REVERT: B 365 MET cc_start: 0.7172 (ppp) cc_final: 0.6830 (ptt) REVERT: B 409 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6386 (ptpp) REVERT: B 449 MET cc_start: 0.7613 (ppp) cc_final: 0.6952 (ppp) REVERT: B 540 ASP cc_start: 0.7866 (t0) cc_final: 0.7478 (t0) REVERT: B 998 TYR cc_start: 0.7867 (p90) cc_final: 0.7635 (p90) REVERT: B 1060 LEU cc_start: 0.8030 (mt) cc_final: 0.7573 (mt) REVERT: B 1084 MET cc_start: 0.7690 (ttt) cc_final: 0.7387 (ttp) REVERT: B 1117 ILE cc_start: 0.8856 (pt) cc_final: 0.8236 (mm) REVERT: B 1136 ASN cc_start: 0.6531 (t0) cc_final: 0.6283 (t0) REVERT: C 131 THR cc_start: 0.7981 (m) cc_final: 0.7393 (p) REVERT: C 236 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7892 (pp) REVERT: D 1 MET cc_start: 0.7242 (tmm) cc_final: 0.6931 (tmm) REVERT: D 117 LYS cc_start: 0.6916 (pmtt) cc_final: 0.6352 (pttt) REVERT: E 58 MET cc_start: 0.6111 (tpt) cc_final: 0.5903 (mmp) REVERT: E 66 GLU cc_start: 0.7567 (tp30) cc_final: 0.7336 (tp30) REVERT: F 85 MET cc_start: 0.8671 (tpp) cc_final: 0.7321 (ttt) REVERT: F 89 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7928 (mt-10) REVERT: F 114 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: G 1 MET cc_start: 0.6317 (ppp) cc_final: 0.5512 (ppp) REVERT: G 50 ASP cc_start: 0.8065 (p0) cc_final: 0.7421 (p0) REVERT: G 170 GLU cc_start: 0.5550 (OUTLIER) cc_final: 0.4056 (tt0) REVERT: H 44 VAL cc_start: 0.8955 (p) cc_final: 0.8623 (t) REVERT: H 146 ARG cc_start: 0.7455 (ppt90) cc_final: 0.6882 (ptt-90) REVERT: I 40 ILE cc_start: 0.3837 (tt) cc_final: 0.3193 (mm) REVERT: K 44 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6526 (ttp-170) REVERT: M 137 GLU cc_start: 0.4380 (OUTLIER) cc_final: 0.3863 (mm-30) REVERT: M 159 TYR cc_start: 0.7261 (m-80) cc_final: 0.7051 (m-10) REVERT: N 279 GLU cc_start: 0.7425 (tt0) cc_final: 0.7126 (tt0) REVERT: N 362 SER cc_start: 0.6011 (OUTLIER) cc_final: 0.5729 (t) REVERT: O 46 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7666 (pp) REVERT: O 60 ARG cc_start: 0.6374 (ptp-170) cc_final: 0.5050 (mmt-90) REVERT: O 565 LEU cc_start: 0.7397 (pt) cc_final: 0.7082 (mp) REVERT: P 146 LYS cc_start: 0.4448 (OUTLIER) cc_final: 0.4123 (mttt) REVERT: V 298 MET cc_start: 0.7096 (mpp) cc_final: 0.6818 (mpp) REVERT: V 334 GLU cc_start: 0.6803 (pt0) cc_final: 0.5397 (mm-30) REVERT: V 464 LYS cc_start: 0.4801 (OUTLIER) cc_final: 0.3555 (pttp) REVERT: V 483 GLU cc_start: 0.4617 (OUTLIER) cc_final: 0.4161 (pt0) REVERT: Y 103 ILE cc_start: 0.4129 (mp) cc_final: 0.3382 (mp) REVERT: Y 104 MET cc_start: 0.7295 (pmm) cc_final: 0.4177 (ttt) REVERT: Y 152 PHE cc_start: 0.2741 (t80) cc_final: 0.2468 (t80) REVERT: Z 164 MET cc_start: 0.6380 (ppp) cc_final: 0.5296 (mmm) REVERT: Z 235 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6733 (t0) REVERT: Z 294 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.6540 (tpt170) outliers start: 331 outliers final: 200 residues processed: 1047 average time/residue: 0.5580 time to fit residues: 988.8620 Evaluate side-chains 932 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 715 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 1003 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1342 THR Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 200 CYS Chi-restraints excluded: chain G residue 210 TRP Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 364 ILE Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 518 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 647 LEU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 146 LYS Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain V residue 335 GLU Chi-restraints excluded: chain V residue 398 ASP Chi-restraints excluded: chain V residue 402 PHE Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain V residue 487 GLU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 100 ILE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 145 ASP Chi-restraints excluded: chain Z residue 162 LEU Chi-restraints excluded: chain Z residue 182 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 480 optimal weight: 7.9990 chunk 327 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 429 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 492 optimal weight: 0.4980 chunk 398 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 chunk 517 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN B 80 ASN B 225 HIS B 396 ASN B 427 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 652 GLN P 205 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 49995 Z= 0.303 Angle : 0.776 13.017 67876 Z= 0.397 Chirality : 0.047 0.232 7580 Planarity : 0.005 0.079 8407 Dihedral : 15.038 168.753 7654 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.07 % Favored : 83.70 % Rotamer: Outliers : 6.43 % Allowed : 20.63 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.25 % 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: -3.26 (0.10), residues: 5885 helix: -0.43 (0.11), residues: 2098 sheet: -2.45 (0.23), residues: 433 loop : -3.49 (0.10), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 31 HIS 0.022 0.002 HIS B 225 PHE 0.033 0.002 PHE B 587 TYR 0.027 0.002 TYR M 131 ARG 0.012 0.001 ARG B 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 784 time to evaluate : 5.970 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 38 ASP cc_start: 0.6198 (m-30) cc_final: 0.5970 (m-30) REVERT: A 146 ASP cc_start: 0.6735 (p0) cc_final: 0.6022 (t70) REVERT: A 184 ARG cc_start: 0.7367 (tmt-80) cc_final: 0.6892 (tmt-80) REVERT: A 202 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7361 (ttmm) REVERT: A 235 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8491 (pttp) REVERT: A 809 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.7712 (mpp) REVERT: A 861 PHE cc_start: 0.8231 (t80) cc_final: 0.8018 (t80) REVERT: A 1051 ASN cc_start: 0.7619 (p0) cc_final: 0.7335 (t0) REVERT: A 1052 VAL cc_start: 0.8504 (t) cc_final: 0.8246 (m) REVERT: A 1082 ARG cc_start: 0.8301 (ttm110) cc_final: 0.8037 (ttm110) REVERT: A 1278 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7980 (mm) REVERT: A 1394 ASP cc_start: 0.7443 (p0) cc_final: 0.7214 (p0) REVERT: B 176 GLU cc_start: 0.7549 (pp20) cc_final: 0.7315 (pp20) REVERT: B 185 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7212 (p90) REVERT: B 271 LEU cc_start: 0.7048 (tp) cc_final: 0.6702 (tp) REVERT: B 325 GLU cc_start: 0.6313 (mp0) cc_final: 0.4609 (mp0) REVERT: B 365 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.7021 (ptt) REVERT: B 409 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6233 (ptpp) REVERT: B 540 ASP cc_start: 0.8027 (t0) cc_final: 0.7698 (t0) REVERT: B 645 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9013 (mm) REVERT: B 652 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7564 (p0) REVERT: B 837 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: B 998 TYR cc_start: 0.7754 (p90) cc_final: 0.7534 (p90) REVERT: B 1060 LEU cc_start: 0.8023 (mt) cc_final: 0.7662 (mt) REVERT: B 1084 MET cc_start: 0.7760 (ttt) cc_final: 0.7312 (ttp) REVERT: B 1117 ILE cc_start: 0.8812 (pt) cc_final: 0.8189 (mm) REVERT: C 131 THR cc_start: 0.8188 (m) cc_final: 0.7591 (p) REVERT: C 236 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7879 (pp) REVERT: D 14 TYR cc_start: 0.5866 (t80) cc_final: 0.5501 (t80) REVERT: D 117 LYS cc_start: 0.7055 (pmtt) cc_final: 0.6352 (pttt) REVERT: F 85 MET cc_start: 0.8650 (tpp) cc_final: 0.7286 (ttt) REVERT: F 89 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8027 (mt-10) REVERT: G 1 MET cc_start: 0.6260 (ppp) cc_final: 0.5841 (ppp) REVERT: G 50 ASP cc_start: 0.8051 (p0) cc_final: 0.7472 (p0) REVERT: G 170 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.4231 (tt0) REVERT: H 44 VAL cc_start: 0.8914 (p) cc_final: 0.8634 (t) REVERT: H 146 ARG cc_start: 0.7558 (ppt90) cc_final: 0.6950 (ptt-90) REVERT: I 1 MET cc_start: 0.4308 (ttm) cc_final: 0.4097 (mtm) REVERT: K 44 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6542 (ttp-170) REVERT: M 137 GLU cc_start: 0.4470 (OUTLIER) cc_final: 0.3988 (mm-30) REVERT: M 226 ARG cc_start: 0.5850 (mtt180) cc_final: 0.5540 (tpt170) REVERT: N 300 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5864 (mmmt) REVERT: O 60 ARG cc_start: 0.6516 (ptp-170) cc_final: 0.5397 (mmt-90) REVERT: O 277 THR cc_start: 0.4877 (OUTLIER) cc_final: 0.4633 (m) REVERT: O 318 LEU cc_start: 0.8300 (mm) cc_final: 0.8076 (tp) REVERT: O 368 ARG cc_start: 0.6931 (ttp80) cc_final: 0.6725 (ttp80) REVERT: O 565 LEU cc_start: 0.7321 (pt) cc_final: 0.7055 (mp) REVERT: O 577 MET cc_start: 0.7997 (tpp) cc_final: 0.7129 (tpp) REVERT: V 298 MET cc_start: 0.7019 (mpp) cc_final: 0.6809 (mpp) REVERT: V 333 GLU cc_start: 0.5940 (mt-10) cc_final: 0.5560 (tt0) REVERT: V 460 ASN cc_start: 0.3791 (m-40) cc_final: 0.3097 (m-40) REVERT: V 464 LYS cc_start: 0.5064 (OUTLIER) cc_final: 0.3808 (pttp) REVERT: V 483 GLU cc_start: 0.4691 (OUTLIER) cc_final: 0.4265 (pt0) REVERT: V 487 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5597 (tt0) REVERT: Y 104 MET cc_start: 0.7239 (pmm) cc_final: 0.4140 (ttt) REVERT: Y 152 PHE cc_start: 0.2807 (t80) cc_final: 0.2585 (t80) REVERT: Z 164 MET cc_start: 0.6654 (ppp) cc_final: 0.5378 (mmp) REVERT: Z 235 ASN cc_start: 0.7119 (OUTLIER) cc_final: 0.6705 (t0) REVERT: Z 294 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.6535 (tpt170) outliers start: 329 outliers final: 222 residues processed: 1028 average time/residue: 0.5670 time to fit residues: 984.7040 Evaluate side-chains 959 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 717 time to evaluate : 5.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1003 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1174 GLN Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 993 ASP Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 200 CYS Chi-restraints excluded: chain G residue 210 TRP Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 300 LYS Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 518 SER Chi-restraints excluded: chain O residue 535 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 647 LEU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain V residue 335 GLU Chi-restraints excluded: chain V residue 402 PHE Chi-restraints excluded: chain V residue 432 LEU Chi-restraints excluded: chain V residue 445 LEU Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain V residue 487 GLU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 100 ILE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 124 ASN Chi-restraints excluded: chain Z residue 128 SER Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 162 LEU Chi-restraints excluded: chain Z residue 182 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 205 LEU Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 244 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 194 optimal weight: 0.9990 chunk 519 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 338 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 577 optimal weight: 9.9990 chunk 479 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 184 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 49995 Z= 0.227 Angle : 0.741 12.306 67876 Z= 0.376 Chirality : 0.045 0.350 7580 Planarity : 0.005 0.079 8407 Dihedral : 14.881 167.028 7654 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.23 % Favored : 83.60 % Rotamer: Outliers : 6.06 % Allowed : 21.90 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.25 % 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: -3.09 (0.11), residues: 5885 helix: -0.22 (0.12), residues: 2102 sheet: -2.25 (0.24), residues: 416 loop : -3.45 (0.10), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 31 HIS 0.011 0.001 HIS B 225 PHE 0.031 0.002 PHE B1018 TYR 0.024 0.002 TYR M 131 ARG 0.009 0.000 ARG B 607 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 780 time to evaluate : 5.268 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 38 ASP cc_start: 0.5987 (m-30) cc_final: 0.5775 (m-30) REVERT: A 146 ASP cc_start: 0.6708 (p0) cc_final: 0.5975 (t70) REVERT: A 184 ARG cc_start: 0.7203 (tmt-80) cc_final: 0.6827 (tmt-80) REVERT: A 202 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7249 (ttmm) REVERT: A 235 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8471 (pttp) REVERT: A 240 GLU cc_start: 0.7882 (tp30) cc_final: 0.7652 (tp30) REVERT: A 372 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7021 (mmm-85) REVERT: A 809 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8051 (mpp) REVERT: A 817 ILE cc_start: 0.5518 (mp) cc_final: 0.5277 (mt) REVERT: A 861 PHE cc_start: 0.8175 (t80) cc_final: 0.7963 (t80) REVERT: A 922 ASP cc_start: 0.8482 (t0) cc_final: 0.8010 (t0) REVERT: A 940 ASP cc_start: 0.7269 (t70) cc_final: 0.7005 (t0) REVERT: A 1052 VAL cc_start: 0.8493 (t) cc_final: 0.8150 (m) REVERT: A 1082 ARG cc_start: 0.8330 (ttm110) cc_final: 0.8029 (ttm110) REVERT: A 1083 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.6930 (tp) REVERT: A 1278 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7916 (mm) REVERT: A 1394 ASP cc_start: 0.7419 (p0) cc_final: 0.7198 (p0) REVERT: B 96 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7112 (t) REVERT: B 185 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7023 (p90) REVERT: B 271 LEU cc_start: 0.6983 (tp) cc_final: 0.6625 (tp) REVERT: B 365 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.7077 (ptt) REVERT: B 409 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6192 (ptpp) REVERT: B 540 ASP cc_start: 0.8065 (t0) cc_final: 0.7571 (t0) REVERT: B 1060 LEU cc_start: 0.7971 (mt) cc_final: 0.7571 (mt) REVERT: B 1084 MET cc_start: 0.7666 (ttt) cc_final: 0.7271 (ttp) REVERT: B 1117 ILE cc_start: 0.8760 (pt) cc_final: 0.8303 (mp) REVERT: C 131 THR cc_start: 0.8230 (m) cc_final: 0.7874 (p) REVERT: D 117 LYS cc_start: 0.7059 (pmtt) cc_final: 0.6270 (pttt) REVERT: E 93 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7285 (ttt) REVERT: F 89 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8064 (tp30) REVERT: G 1 MET cc_start: 0.6141 (ppp) cc_final: 0.5780 (ppp) REVERT: G 50 ASP cc_start: 0.8021 (p0) cc_final: 0.7482 (p0) REVERT: G 170 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.4269 (tt0) REVERT: H 44 VAL cc_start: 0.8927 (p) cc_final: 0.8645 (t) REVERT: H 146 ARG cc_start: 0.7583 (ppt90) cc_final: 0.6873 (ptt-90) REVERT: K 44 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6306 (ttp-170) REVERT: M 137 GLU cc_start: 0.4399 (OUTLIER) cc_final: 0.3898 (mm-30) REVERT: M 190 ASN cc_start: 0.6369 (OUTLIER) cc_final: 0.5265 (t0) REVERT: M 226 ARG cc_start: 0.5766 (mtt180) cc_final: 0.5383 (tpt170) REVERT: N 362 SER cc_start: 0.6427 (OUTLIER) cc_final: 0.6138 (t) REVERT: O 60 ARG cc_start: 0.6466 (ptp-170) cc_final: 0.5381 (mmt-90) REVERT: O 103 CYS cc_start: 0.7116 (m) cc_final: 0.6532 (m) REVERT: O 577 MET cc_start: 0.7949 (tpp) cc_final: 0.7056 (tpp) REVERT: P 86 MET cc_start: -0.0346 (tmm) cc_final: -0.1959 (tpp) REVERT: P 146 LYS cc_start: 0.4405 (OUTLIER) cc_final: 0.4193 (mttt) REVERT: V 460 ASN cc_start: 0.3701 (m-40) cc_final: 0.3032 (m-40) REVERT: V 464 LYS cc_start: 0.4833 (OUTLIER) cc_final: 0.3781 (pttp) REVERT: V 483 GLU cc_start: 0.4679 (OUTLIER) cc_final: 0.4292 (pt0) REVERT: Y 104 MET cc_start: 0.7247 (pmm) cc_final: 0.4177 (ttt) REVERT: Y 152 PHE cc_start: 0.2883 (t80) cc_final: 0.2640 (t80) REVERT: Z 123 GLN cc_start: 0.6477 (mt0) cc_final: 0.6136 (mp10) REVERT: Z 142 MET cc_start: 0.7683 (ppp) cc_final: 0.7135 (ppp) REVERT: Z 164 MET cc_start: 0.6563 (ppp) cc_final: 0.5280 (mmp) REVERT: Z 235 ASN cc_start: 0.7072 (OUTLIER) cc_final: 0.6669 (t0) REVERT: Z 294 ARG cc_start: 0.7300 (ttp-110) cc_final: 0.6493 (tpt170) outliers start: 310 outliers final: 217 residues processed: 1002 average time/residue: 0.5674 time to fit residues: 961.7969 Evaluate side-chains 957 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 720 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1003 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1342 THR Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 137 TYR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 200 CYS Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 374 LYS Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 370 LEU Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 535 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 647 LEU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 146 LYS Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 149 MET Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain V residue 335 GLU Chi-restraints excluded: chain V residue 402 PHE Chi-restraints excluded: chain V residue 437 THR Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 100 ILE Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 124 ASN Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 162 LEU Chi-restraints excluded: chain Z residue 182 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 453 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 556 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 421 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 chunk 486 optimal weight: 4.9990 chunk 322 optimal weight: 0.6980 chunk 575 optimal weight: 0.3980 chunk 360 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 427 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN P 59 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 49995 Z= 0.276 Angle : 0.772 15.861 67876 Z= 0.392 Chirality : 0.047 0.325 7580 Planarity : 0.005 0.084 8407 Dihedral : 14.858 164.645 7654 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.84 % Favored : 82.97 % Rotamer: Outliers : 6.74 % Allowed : 22.13 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.23 % 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: -3.08 (0.11), residues: 5885 helix: -0.18 (0.12), residues: 2102 sheet: -2.31 (0.23), residues: 452 loop : -3.47 (0.10), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 31 HIS 0.008 0.001 HIS Z 140 PHE 0.030 0.002 PHE B1018 TYR 0.026 0.002 TYR M 131 ARG 0.008 0.001 ARG B 607 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 734 time to evaluate : 5.665 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 146 ASP cc_start: 0.6785 (p0) cc_final: 0.5959 (t70) REVERT: A 184 ARG cc_start: 0.7283 (tmt-80) cc_final: 0.6829 (tmt-80) REVERT: A 202 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7401 (ttmm) REVERT: A 235 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8451 (pttp) REVERT: A 240 GLU cc_start: 0.7937 (tp30) cc_final: 0.7720 (tp30) REVERT: A 372 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7074 (mmm-85) REVERT: A 809 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.7879 (mpp) REVERT: A 817 ILE cc_start: 0.5580 (mp) cc_final: 0.5347 (mt) REVERT: A 861 PHE cc_start: 0.8187 (t80) cc_final: 0.7912 (t80) REVERT: A 922 ASP cc_start: 0.8466 (t0) cc_final: 0.8051 (t0) REVERT: A 1082 ARG cc_start: 0.8255 (ttm110) cc_final: 0.8038 (ttm110) REVERT: A 1083 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.6913 (tp) REVERT: A 1403 MET cc_start: 0.8378 (mtt) cc_final: 0.8125 (mtp) REVERT: B 185 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7214 (p90) REVERT: B 271 LEU cc_start: 0.7095 (tp) cc_final: 0.6776 (tp) REVERT: B 325 GLU cc_start: 0.6538 (mp0) cc_final: 0.4756 (mp0) REVERT: B 365 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7229 (ptt) REVERT: B 409 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6112 (ptpp) REVERT: B 837 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: B 1060 LEU cc_start: 0.8003 (mt) cc_final: 0.7577 (mt) REVERT: B 1084 MET cc_start: 0.7870 (ttt) cc_final: 0.7415 (ttp) REVERT: B 1117 ILE cc_start: 0.8784 (pt) cc_final: 0.8141 (mm) REVERT: C 57 ILE cc_start: 0.5199 (tp) cc_final: 0.4947 (mm) REVERT: C 131 THR cc_start: 0.8264 (m) cc_final: 0.7789 (p) REVERT: C 236 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7978 (pp) REVERT: D 117 LYS cc_start: 0.6691 (pmtt) cc_final: 0.6079 (pttt) REVERT: D 122 GLN cc_start: 0.6144 (tp-100) cc_final: 0.5920 (tp40) REVERT: E 93 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7246 (ttt) REVERT: F 127 GLU cc_start: 0.6760 (tp30) cc_final: 0.6493 (tp30) REVERT: G 1 MET cc_start: 0.6192 (ppp) cc_final: 0.5867 (ppp) REVERT: G 50 ASP cc_start: 0.8094 (p0) cc_final: 0.7520 (p0) REVERT: G 170 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.4423 (tt0) REVERT: H 44 VAL cc_start: 0.8912 (p) cc_final: 0.8682 (t) REVERT: H 146 ARG cc_start: 0.7474 (ppt90) cc_final: 0.6892 (ptt-90) REVERT: K 44 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6350 (ttp-170) REVERT: M 137 GLU cc_start: 0.4296 (OUTLIER) cc_final: 0.3833 (mm-30) REVERT: M 190 ASN cc_start: 0.6411 (OUTLIER) cc_final: 0.5287 (t0) REVERT: N 362 SER cc_start: 0.6530 (OUTLIER) cc_final: 0.6163 (t) REVERT: O 32 MET cc_start: 0.4504 (mtt) cc_final: 0.3983 (mtm) REVERT: O 49 TYR cc_start: 0.8684 (m-80) cc_final: 0.8480 (m-10) REVERT: O 60 ARG cc_start: 0.6551 (ptp-170) cc_final: 0.5363 (mmt-90) REVERT: O 103 CYS cc_start: 0.7234 (m) cc_final: 0.6816 (m) REVERT: O 493 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6478 (mm-30) REVERT: O 516 LEU cc_start: 0.6128 (tt) cc_final: 0.5837 (tt) REVERT: O 543 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6552 (m-80) REVERT: O 565 LEU cc_start: 0.7367 (tt) cc_final: 0.6428 (mp) REVERT: P 86 MET cc_start: -0.0246 (OUTLIER) cc_final: -0.1805 (tpp) REVERT: Q 58 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.5014 (t80) REVERT: V 408 TYR cc_start: 0.4437 (m-80) cc_final: 0.4162 (m-80) REVERT: V 460 ASN cc_start: 0.3806 (m-40) cc_final: 0.3297 (m-40) REVERT: V 464 LYS cc_start: 0.5081 (OUTLIER) cc_final: 0.3848 (pttp) REVERT: V 483 GLU cc_start: 0.4479 (OUTLIER) cc_final: 0.4018 (pt0) REVERT: Y 104 MET cc_start: 0.7139 (pmm) cc_final: 0.4123 (ttt) REVERT: Y 152 PHE cc_start: 0.3441 (t80) cc_final: 0.3124 (t80) REVERT: Z 123 GLN cc_start: 0.6520 (mt0) cc_final: 0.6117 (mp10) REVERT: Z 142 MET cc_start: 0.7588 (ppp) cc_final: 0.7363 (ppp) REVERT: Z 164 MET cc_start: 0.6301 (ppp) cc_final: 0.5426 (mmp) REVERT: Z 235 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6709 (t0) REVERT: Z 294 ARG cc_start: 0.7263 (ttp-110) cc_final: 0.6445 (tpt170) outliers start: 345 outliers final: 244 residues processed: 987 average time/residue: 0.5563 time to fit residues: 932.0855 Evaluate side-chains 961 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 695 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1003 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1342 THR Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 155 PHE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 374 LYS Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 370 LEU Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 518 SER Chi-restraints excluded: chain O residue 543 TYR Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 579 GLN Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 647 LEU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 146 LYS Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 149 MET Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain V residue 335 GLU Chi-restraints excluded: chain V residue 402 PHE Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain V residue 487 GLU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 100 ILE Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 162 LEU Chi-restraints excluded: chain Z residue 182 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 453 SER Chi-restraints excluded: chain Z residue 469 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 355 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 392 optimal weight: 7.9990 chunk 284 optimal weight: 3.9990 chunk 53 optimal weight: 0.0770 chunk 452 optimal weight: 9.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN I 9 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN O 584 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 207 GLN Z 241 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 49995 Z= 0.288 Angle : 0.782 15.465 67876 Z= 0.397 Chirality : 0.047 0.307 7580 Planarity : 0.005 0.078 8407 Dihedral : 14.883 162.561 7654 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.94 % Favored : 82.87 % Rotamer: Outliers : 6.37 % Allowed : 22.89 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.21 % 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: -3.07 (0.11), residues: 5885 helix: -0.18 (0.11), residues: 2109 sheet: -2.27 (0.23), residues: 442 loop : -3.46 (0.10), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 31 HIS 0.012 0.001 HIS K 95 PHE 0.049 0.002 PHE B 342 TYR 0.032 0.002 TYR D 135 ARG 0.008 0.001 ARG B 607 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 709 time to evaluate : 5.627 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: A 1 MET cc_start: 0.5266 (tmm) cc_final: 0.4864 (tmm) REVERT: A 146 ASP cc_start: 0.6662 (p0) cc_final: 0.5842 (t70) REVERT: A 184 ARG cc_start: 0.7271 (tmt-80) cc_final: 0.6805 (tmt-80) REVERT: A 202 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7455 (ttmm) REVERT: A 235 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8403 (pttp) REVERT: A 372 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7038 (mmm-85) REVERT: A 516 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: A 716 ASP cc_start: 0.7681 (m-30) cc_final: 0.7452 (m-30) REVERT: A 809 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.7849 (mpp) REVERT: A 861 PHE cc_start: 0.8245 (t80) cc_final: 0.7951 (t80) REVERT: A 922 ASP cc_start: 0.8452 (t0) cc_final: 0.8089 (t0) REVERT: A 1083 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.6874 (tp) REVERT: B 185 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7225 (p90) REVERT: B 271 LEU cc_start: 0.7109 (tp) cc_final: 0.6758 (tp) REVERT: B 325 GLU cc_start: 0.6507 (mp0) cc_final: 0.4836 (mp0) REVERT: B 365 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7376 (ptt) REVERT: B 409 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6302 (ptpp) REVERT: B 652 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7616 (p0) REVERT: B 837 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: B 1060 LEU cc_start: 0.8032 (mt) cc_final: 0.7579 (mt) REVERT: B 1084 MET cc_start: 0.7884 (ttt) cc_final: 0.7359 (ttp) REVERT: B 1117 ILE cc_start: 0.8763 (pt) cc_final: 0.8156 (mm) REVERT: B 1137 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7768 (tt) REVERT: C 57 ILE cc_start: 0.5193 (tp) cc_final: 0.4935 (mm) REVERT: C 236 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7998 (pp) REVERT: D 117 LYS cc_start: 0.6713 (pmtt) cc_final: 0.6114 (pttt) REVERT: D 153 MET cc_start: 0.6273 (mpp) cc_final: 0.5788 (tpp) REVERT: E 93 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7200 (ttt) REVERT: F 85 MET cc_start: 0.8725 (tpp) cc_final: 0.7703 (ttt) REVERT: F 150 GLU cc_start: 0.5764 (pm20) cc_final: 0.5415 (pm20) REVERT: G 1 MET cc_start: 0.6270 (ppp) cc_final: 0.6038 (ppp) REVERT: G 50 ASP cc_start: 0.8070 (p0) cc_final: 0.7543 (p0) REVERT: G 104 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.7047 (mm) REVERT: G 170 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.4263 (tt0) REVERT: H 44 VAL cc_start: 0.8939 (p) cc_final: 0.8682 (t) REVERT: H 146 ARG cc_start: 0.7504 (ppt90) cc_final: 0.6926 (ptt-90) REVERT: I 1 MET cc_start: 0.5089 (mtm) cc_final: 0.4799 (mtm) REVERT: K 44 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6260 (ttp-170) REVERT: M 92 ASN cc_start: 0.6505 (OUTLIER) cc_final: 0.6124 (t0) REVERT: M 190 ASN cc_start: 0.6310 (OUTLIER) cc_final: 0.5160 (t0) REVERT: N 362 SER cc_start: 0.6564 (OUTLIER) cc_final: 0.6204 (t) REVERT: O 32 MET cc_start: 0.4593 (mtt) cc_final: 0.4028 (mtm) REVERT: O 60 ARG cc_start: 0.6526 (ptp-170) cc_final: 0.5401 (mmt-90) REVERT: O 103 CYS cc_start: 0.7281 (m) cc_final: 0.6871 (m) REVERT: O 144 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5936 (mpp) REVERT: O 516 LEU cc_start: 0.6258 (tt) cc_final: 0.6028 (tt) REVERT: O 543 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: O 577 MET cc_start: 0.7833 (tpp) cc_final: 0.7239 (tpp) REVERT: P 86 MET cc_start: -0.0306 (OUTLIER) cc_final: -0.1182 (tpp) REVERT: P 146 LYS cc_start: 0.5041 (OUTLIER) cc_final: 0.4743 (mtmt) REVERT: Q 58 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.5068 (t80) REVERT: V 408 TYR cc_start: 0.4553 (m-80) cc_final: 0.4222 (m-80) REVERT: V 460 ASN cc_start: 0.3805 (m-40) cc_final: 0.3158 (m-40) REVERT: V 464 LYS cc_start: 0.5221 (OUTLIER) cc_final: 0.3977 (pttp) REVERT: V 483 GLU cc_start: 0.4566 (OUTLIER) cc_final: 0.4114 (pt0) REVERT: V 487 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5636 (tt0) REVERT: Y 93 GLU cc_start: 0.6177 (tt0) cc_final: 0.5881 (tt0) REVERT: Y 104 MET cc_start: 0.7276 (pmm) cc_final: 0.4142 (ttt) REVERT: Y 152 PHE cc_start: 0.3319 (t80) cc_final: 0.3067 (t80) REVERT: Z 142 MET cc_start: 0.7612 (ppp) cc_final: 0.7410 (ppp) REVERT: Z 147 SER cc_start: 0.8781 (t) cc_final: 0.8300 (p) REVERT: Z 164 MET cc_start: 0.6355 (ppp) cc_final: 0.5312 (mmp) REVERT: Z 235 ASN cc_start: 0.7000 (OUTLIER) cc_final: 0.6658 (t0) REVERT: Z 245 VAL cc_start: 0.7238 (t) cc_final: 0.6832 (p) REVERT: Z 294 ARG cc_start: 0.7317 (ttp-110) cc_final: 0.6398 (tpt170) outliers start: 326 outliers final: 250 residues processed: 954 average time/residue: 0.5626 time to fit residues: 909.9158 Evaluate side-chains 958 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 679 time to evaluate : 5.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1003 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1163 LYS Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1342 THR Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 155 PHE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 131 TYR Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 374 LYS Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 370 LEU Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 518 SER Chi-restraints excluded: chain O residue 543 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 579 GLN Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 647 LEU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 146 LYS Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 149 MET Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain V residue 335 GLU Chi-restraints excluded: chain V residue 402 PHE Chi-restraints excluded: chain V residue 437 THR Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain V residue 487 GLU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 100 ILE Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 124 ASN Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 162 LEU Chi-restraints excluded: chain Z residue 182 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 453 SER Chi-restraints excluded: chain Z residue 469 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 523 optimal weight: 9.9990 chunk 551 optimal weight: 0.9980 chunk 502 optimal weight: 0.2980 chunk 536 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 421 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 484 optimal weight: 3.9990 chunk 507 optimal weight: 0.8980 chunk 534 optimal weight: 0.0040 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 GLN B 270 GLN B 427 ASN B 595 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 392 GLN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 HIS O 207 HIS ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 584 ASN ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 49995 Z= 0.190 Angle : 0.748 15.118 67876 Z= 0.375 Chirality : 0.045 0.346 7580 Planarity : 0.004 0.079 8407 Dihedral : 14.740 161.296 7654 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.94 % Favored : 84.89 % Rotamer: Outliers : 4.59 % Allowed : 24.54 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.18 % 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: -2.88 (0.11), residues: 5885 helix: -0.00 (0.12), residues: 2122 sheet: -1.98 (0.25), residues: 420 loop : -3.41 (0.10), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP Z 487 HIS 0.010 0.001 HIS Z 140 PHE 0.047 0.002 PHE B 342 TYR 0.032 0.002 TYR D 135 ARG 0.010 0.000 ARG M 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 777 time to evaluate : 4.516 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 1 MET cc_start: 0.4807 (tmm) cc_final: 0.4486 (tmm) REVERT: A 146 ASP cc_start: 0.6819 (p0) cc_final: 0.5932 (t70) REVERT: A 184 ARG cc_start: 0.7069 (tmt-80) cc_final: 0.6698 (tmt-80) REVERT: A 202 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7253 (ttmm) REVERT: A 235 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8295 (pttp) REVERT: A 303 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6273 (mm) REVERT: A 320 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 372 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6978 (mmm-85) REVERT: A 516 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: A 530 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 577 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7654 (m) REVERT: A 651 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: A 716 ASP cc_start: 0.7471 (m-30) cc_final: 0.7186 (m-30) REVERT: A 809 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7794 (mpp) REVERT: A 861 PHE cc_start: 0.7988 (t80) cc_final: 0.7727 (t80) REVERT: A 922 ASP cc_start: 0.8432 (t0) cc_final: 0.8032 (t0) REVERT: A 972 GLU cc_start: 0.8000 (tp30) cc_final: 0.7713 (tp30) REVERT: B 185 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6646 (p90) REVERT: B 255 ILE cc_start: 0.8422 (tt) cc_final: 0.8204 (mt) REVERT: B 271 LEU cc_start: 0.6818 (tp) cc_final: 0.6265 (tp) REVERT: B 325 GLU cc_start: 0.6016 (mp0) cc_final: 0.4200 (mp0) REVERT: B 512 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7295 (pmmt) REVERT: B 652 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7571 (p0) REVERT: B 850 ASN cc_start: 0.5926 (p0) cc_final: 0.5423 (p0) REVERT: B 953 MET cc_start: 0.7167 (mmm) cc_final: 0.6924 (mtt) REVERT: B 1035 MET cc_start: 0.8716 (tpp) cc_final: 0.8413 (tpp) REVERT: B 1060 LEU cc_start: 0.7877 (mt) cc_final: 0.7537 (mt) REVERT: B 1084 MET cc_start: 0.7776 (ttt) cc_final: 0.7310 (ttp) REVERT: B 1117 ILE cc_start: 0.8702 (pt) cc_final: 0.8187 (mp) REVERT: D 107 MET cc_start: 0.4859 (tpt) cc_final: 0.4515 (tpt) REVERT: D 117 LYS cc_start: 0.6842 (pmtt) cc_final: 0.5885 (pttp) REVERT: E 93 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7088 (ttt) REVERT: E 159 ASP cc_start: 0.7479 (p0) cc_final: 0.6569 (p0) REVERT: F 89 GLU cc_start: 0.8678 (tp30) cc_final: 0.8324 (mm-30) REVERT: G 1 MET cc_start: 0.6207 (ppp) cc_final: 0.5963 (ppp) REVERT: G 50 ASP cc_start: 0.8006 (p0) cc_final: 0.7554 (p0) REVERT: G 67 TYR cc_start: 0.7357 (m-80) cc_final: 0.7055 (m-80) REVERT: G 170 GLU cc_start: 0.5626 (OUTLIER) cc_final: 0.3989 (tt0) REVERT: G 173 GLN cc_start: 0.6598 (mp10) cc_final: 0.6363 (mp10) REVERT: H 44 VAL cc_start: 0.8906 (p) cc_final: 0.8705 (t) REVERT: H 146 ARG cc_start: 0.7488 (ppt90) cc_final: 0.7202 (ttp80) REVERT: M 190 ASN cc_start: 0.6452 (OUTLIER) cc_final: 0.5534 (t0) REVERT: M 226 ARG cc_start: 0.5661 (OUTLIER) cc_final: 0.5367 (tpt170) REVERT: O 32 MET cc_start: 0.4485 (mtt) cc_final: 0.3971 (mtm) REVERT: O 49 TYR cc_start: 0.8648 (m-10) cc_final: 0.8347 (m-10) REVERT: O 60 ARG cc_start: 0.6400 (ptp-170) cc_final: 0.5262 (mmt-90) REVERT: O 103 CYS cc_start: 0.7163 (m) cc_final: 0.6723 (m) REVERT: O 220 GLU cc_start: 0.7031 (pp20) cc_final: 0.6630 (pp20) REVERT: O 565 LEU cc_start: 0.6920 (tt) cc_final: 0.6115 (mp) REVERT: O 577 MET cc_start: 0.7802 (tpp) cc_final: 0.7337 (tpp) REVERT: P 77 GLU cc_start: 0.4588 (tm-30) cc_final: 0.3848 (mm-30) REVERT: P 86 MET cc_start: -0.0711 (tmm) cc_final: -0.2196 (tpp) REVERT: Q 58 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.4795 (t80) REVERT: V 293 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.5436 (m-80) REVERT: V 408 TYR cc_start: 0.4295 (m-80) cc_final: 0.4093 (m-80) REVERT: V 460 ASN cc_start: 0.3597 (m-40) cc_final: 0.3145 (m-40) REVERT: V 464 LYS cc_start: 0.5052 (OUTLIER) cc_final: 0.4368 (pptt) REVERT: V 483 GLU cc_start: 0.4380 (OUTLIER) cc_final: 0.3969 (pt0) REVERT: Y 104 MET cc_start: 0.7088 (pmm) cc_final: 0.4102 (ttt) REVERT: Y 152 PHE cc_start: 0.3200 (t80) cc_final: 0.2905 (t80) REVERT: Z 147 SER cc_start: 0.8697 (t) cc_final: 0.8232 (p) REVERT: Z 164 MET cc_start: 0.6113 (ppp) cc_final: 0.5341 (mmp) REVERT: Z 235 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6629 (t0) REVERT: Z 245 VAL cc_start: 0.7371 (t) cc_final: 0.6944 (p) REVERT: Z 294 ARG cc_start: 0.7064 (ttp-110) cc_final: 0.6313 (tpt170) outliers start: 235 outliers final: 173 residues processed: 945 average time/residue: 0.6082 time to fit residues: 978.2519 Evaluate side-chains 891 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 698 time to evaluate : 6.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1163 LYS Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 155 PHE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain M residue 131 TYR Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 370 LEU Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 518 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 579 GLN Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 149 MET Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain V residue 293 PHE Chi-restraints excluded: chain V residue 335 GLU Chi-restraints excluded: chain V residue 402 PHE Chi-restraints excluded: chain V residue 437 THR Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 162 LEU Chi-restraints excluded: chain Z residue 182 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 212 ASP Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 453 SER Chi-restraints excluded: chain Z residue 469 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 352 optimal weight: 6.9990 chunk 567 optimal weight: 6.9990 chunk 346 optimal weight: 0.4980 chunk 268 optimal weight: 5.9990 chunk 394 optimal weight: 0.3980 chunk 594 optimal weight: 10.0000 chunk 547 optimal weight: 0.3980 chunk 473 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 365 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 GLN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 332 GLN ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 49995 Z= 0.216 Angle : 0.764 14.569 67876 Z= 0.383 Chirality : 0.046 0.345 7580 Planarity : 0.005 0.079 8407 Dihedral : 14.735 161.341 7654 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 15.75 % Favored : 84.04 % Rotamer: Outliers : 4.22 % Allowed : 25.30 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.16 % 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: -2.84 (0.11), residues: 5885 helix: 0.03 (0.12), residues: 2128 sheet: -1.99 (0.24), residues: 454 loop : -3.38 (0.10), residues: 3303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP V 435 HIS 0.010 0.001 HIS Z 140 PHE 0.046 0.002 PHE B 342 TYR 0.039 0.002 TYR P 215 ARG 0.009 0.000 ARG B 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 714 time to evaluate : 5.552 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 1 MET cc_start: 0.4929 (tmm) cc_final: 0.4690 (tmm) REVERT: A 146 ASP cc_start: 0.6744 (p0) cc_final: 0.5889 (t70) REVERT: A 184 ARG cc_start: 0.7099 (tmt-80) cc_final: 0.6708 (tmt-80) REVERT: A 202 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7235 (ttmm) REVERT: A 235 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8201 (pttp) REVERT: A 372 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6949 (mmm-85) REVERT: A 516 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: A 809 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7649 (mpp) REVERT: A 861 PHE cc_start: 0.8111 (t80) cc_final: 0.7787 (t80) REVERT: B 185 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6832 (p90) REVERT: B 325 GLU cc_start: 0.6142 (mp0) cc_final: 0.4283 (mp0) REVERT: B 652 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7653 (p0) REVERT: B 850 ASN cc_start: 0.6099 (p0) cc_final: 0.5583 (p0) REVERT: B 931 MET cc_start: 0.8421 (mmt) cc_final: 0.8188 (mmt) REVERT: B 953 MET cc_start: 0.7294 (mmm) cc_final: 0.6988 (mtt) REVERT: B 1035 MET cc_start: 0.8703 (tpp) cc_final: 0.8381 (tpp) REVERT: B 1060 LEU cc_start: 0.7940 (mt) cc_final: 0.7574 (mt) REVERT: B 1084 MET cc_start: 0.7816 (ttt) cc_final: 0.7305 (ttp) REVERT: B 1117 ILE cc_start: 0.8751 (pt) cc_final: 0.8278 (mp) REVERT: C 7 ILE cc_start: 0.8684 (mm) cc_final: 0.8447 (mm) REVERT: D 107 MET cc_start: 0.4964 (tpt) cc_final: 0.4609 (tpt) REVERT: D 117 LYS cc_start: 0.6863 (pmtt) cc_final: 0.5906 (pttp) REVERT: E 93 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7111 (ttt) REVERT: F 72 LYS cc_start: 0.6380 (mmtt) cc_final: 0.5965 (tttt) REVERT: F 89 GLU cc_start: 0.8540 (tp30) cc_final: 0.8311 (mm-30) REVERT: G 1 MET cc_start: 0.6356 (ppp) cc_final: 0.5893 (ppp) REVERT: G 50 ASP cc_start: 0.8032 (p0) cc_final: 0.7486 (p0) REVERT: G 67 TYR cc_start: 0.7449 (m-80) cc_final: 0.7084 (m-80) REVERT: G 170 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.4048 (tt0) REVERT: H 44 VAL cc_start: 0.8885 (p) cc_final: 0.8679 (t) REVERT: H 146 ARG cc_start: 0.7552 (ppt90) cc_final: 0.7269 (ttp80) REVERT: M 92 ASN cc_start: 0.6314 (OUTLIER) cc_final: 0.5830 (t0) REVERT: M 190 ASN cc_start: 0.6524 (OUTLIER) cc_final: 0.5472 (t0) REVERT: O 32 MET cc_start: 0.4538 (mtt) cc_final: 0.4017 (mtm) REVERT: O 49 TYR cc_start: 0.8532 (m-10) cc_final: 0.8323 (m-10) REVERT: O 60 ARG cc_start: 0.6521 (ptp-170) cc_final: 0.5381 (mmt-90) REVERT: O 103 CYS cc_start: 0.7241 (m) cc_final: 0.6873 (m) REVERT: O 565 LEU cc_start: 0.7237 (tt) cc_final: 0.6281 (mp) REVERT: O 577 MET cc_start: 0.7878 (tpp) cc_final: 0.7269 (tpp) REVERT: P 77 GLU cc_start: 0.4644 (tm-30) cc_final: 0.3898 (mm-30) REVERT: P 86 MET cc_start: -0.0657 (tmm) cc_final: -0.1415 (tpp) REVERT: P 146 LYS cc_start: 0.4933 (mttt) cc_final: 0.4509 (mtmt) REVERT: Q 58 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.4852 (t80) REVERT: V 293 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.5535 (m-80) REVERT: V 460 ASN cc_start: 0.3680 (m-40) cc_final: 0.3267 (m-40) REVERT: V 464 LYS cc_start: 0.4838 (OUTLIER) cc_final: 0.4271 (pptt) REVERT: V 483 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.3988 (pt0) REVERT: Y 93 GLU cc_start: 0.5667 (tt0) cc_final: 0.5412 (tt0) REVERT: Y 104 MET cc_start: 0.6981 (pmm) cc_final: 0.3897 (ttt) REVERT: Y 152 PHE cc_start: 0.3278 (t80) cc_final: 0.2993 (t80) REVERT: Z 124 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6712 (m-40) REVERT: Z 142 MET cc_start: 0.7210 (ppp) cc_final: 0.6700 (ppp) REVERT: Z 144 ILE cc_start: 0.8066 (mm) cc_final: 0.7773 (mm) REVERT: Z 164 MET cc_start: 0.6266 (ppp) cc_final: 0.5375 (mmp) REVERT: Z 235 ASN cc_start: 0.7000 (OUTLIER) cc_final: 0.6646 (t0) REVERT: Z 245 VAL cc_start: 0.7243 (t) cc_final: 0.6879 (p) REVERT: Z 294 ARG cc_start: 0.7062 (ttp-110) cc_final: 0.6255 (tpt170) outliers start: 216 outliers final: 176 residues processed: 868 average time/residue: 0.6045 time to fit residues: 888.6850 Evaluate side-chains 876 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 683 time to evaluate : 5.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1163 LYS Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 972 THR Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 131 TYR Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 416 ILE Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 234 ASP Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 370 LEU Chi-restraints excluded: chain O residue 482 LYS Chi-restraints excluded: chain O residue 487 LEU Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 518 SER Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 579 GLN Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 602 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 147 ILE Chi-restraints excluded: chain P residue 232 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain V residue 293 PHE Chi-restraints excluded: chain V residue 402 PHE Chi-restraints excluded: chain V residue 437 THR Chi-restraints excluded: chain V residue 464 LYS Chi-restraints excluded: chain V residue 483 GLU Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 122 SER Chi-restraints excluded: chain Z residue 124 ASN Chi-restraints excluded: chain Z residue 162 LEU Chi-restraints excluded: chain Z residue 182 ILE Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 469 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 376 optimal weight: 8.9990 chunk 504 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 436 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 474 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 487 optimal weight: 3.9990 chunk 60 optimal weight: 0.0370 chunk 87 optimal weight: 6.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 225 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 427 ASN B 595 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN I 9 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS O 229 ASN ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 584 ASN P 53 GLN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 407 ASN ** Z 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.145989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124333 restraints weight = 102927.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123896 restraints weight = 128586.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124851 restraints weight = 108713.002| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 49995 Z= 0.359 Angle : 0.855 14.277 67876 Z= 0.435 Chirality : 0.049 0.369 7580 Planarity : 0.006 0.100 8407 Dihedral : 14.996 160.593 7654 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.94 % Favored : 81.80 % Rotamer: Outliers : 4.54 % Allowed : 25.24 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.18 % 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: -3.03 (0.11), residues: 5885 helix: -0.14 (0.11), residues: 2124 sheet: -2.21 (0.22), residues: 482 loop : -3.46 (0.10), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP Z 487 HIS 0.013 0.002 HIS K 95 PHE 0.043 0.002 PHE B 342 TYR 0.047 0.002 TYR B 304 ARG 0.019 0.001 ARG M 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15282.22 seconds wall clock time: 273 minutes 10.02 seconds (16390.02 seconds total)