Starting phenix.real_space_refine on Sun Jun 30 20:04:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbz_19040/06_2024/8rbz_19040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbz_19040/06_2024/8rbz_19040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbz_19040/06_2024/8rbz_19040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbz_19040/06_2024/8rbz_19040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbz_19040/06_2024/8rbz_19040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbz_19040/06_2024/8rbz_19040.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 2 6.06 5 S 410 5.16 5 C 47042 2.51 5 N 12960 2.21 5 O 13686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 74102 Number of models: 1 Model: "" Number of chains: 23 Chain: "1" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 296 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 95 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 4, 'TRANS': 8} Chain: "a" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8525 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 1033} Chain breaks: 11 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "b" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 7988 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 8 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 187 Chain: "c" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3717 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 443} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 6395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6395 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 41, 'TRANS': 776} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "e" Number of atoms: 6253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6253 Classifications: {'peptide': 855} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 53, 'TRANS': 801} Chain breaks: 10 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 171 Chain: "f" Number of atoms: 4137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4137 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 45, 'TRANS': 498} Chain breaks: 6 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 Chain: "g" Number of atoms: 6725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 6725 Classifications: {'peptide': 886} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 29, 'TRANS': 856} Chain breaks: 4 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "h" Number of atoms: 6748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 887, 6748 Classifications: {'peptide': 887} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 32, 'TRANS': 854} Chain breaks: 10 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 9, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 234 Chain: "i" Number of atoms: 4867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4867 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 47, 'TRANS': 578} Chain breaks: 3 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "j" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 3313 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 599} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 648} Chain breaks: 3 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2247 Unresolved non-hydrogen angles: 2873 Unresolved non-hydrogen dihedrals: 1878 Unresolved non-hydrogen chiralities: 198 Planarities with less than four sites: {'GLN:plan1': 37, 'HIS:plan': 17, 'TYR:plan': 24, 'ASN:plan1': 33, 'TRP:plan': 10, 'ASP:plan': 29, 'PHE:plan': 31, 'GLU:plan': 51, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1272 Chain: "k" Number of atoms: 4079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4079 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 25, 'TRANS': 525} Chain breaks: 5 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 192 Chain: "n" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1007 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 182} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 195} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 792 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 9, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 324 Chain: "o" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 1824 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 331} Link IDs: {'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1446 Unresolved non-hydrogen dihedrals: 920 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 21, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 13, 'GLU:plan': 18, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 556 Chain: "p" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4432 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 26, 'TRANS': 553} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "q" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2322 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 278} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "r" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 237 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "m" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 287 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 29.92, per 1000 atoms: 0.40 Number of scatterers: 74102 At special positions: 0 Unit cell: (240.45, 233.1, 266.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Mn 2 24.99 S 410 16.00 O 13686 8.00 N 12960 7.00 C 47042 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: 23.97 Conformation dependent library (CDL) restraints added in 10.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN k1001 " pdb="ZN ZN k1001 " - pdb=" NE2 HIS k 68 " pdb="ZN ZN k1001 " - pdb=" NE2 HIS k 73 " pdb="ZN ZN k1001 " - pdb="ZN ZN k1002 " pdb=" ZN k1002 " pdb="ZN ZN k1002 " - pdb=" NE2 HIS k 68 " pdb="ZN ZN k1002 " - pdb=" ND1 HIS k 70 " pdb="ZN ZN k1002 " - pdb=" NE2 HIS k 157 " 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19310 Finding SS restraints... Secondary structure from input PDB file: 540 helices and 31 sheets defined 69.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.585A pdb=" N ASP B 9 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 10 " --> pdb=" O VAL B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 6 through 10' Processing helix chain 'B' and resid 55 through 62 removed outlier: 3.826A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'a' and resid 947 through 960 Processing helix chain 'a' and resid 964 through 977 removed outlier: 3.561A pdb=" N PHE a 975 " --> pdb=" O VAL a 971 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG a 977 " --> pdb=" O ASP a 973 " (cutoff:3.500A) Processing helix chain 'a' and resid 983 through 999 Processing helix chain 'a' and resid 1023 through 1025 No H-bonds generated for 'chain 'a' and resid 1023 through 1025' Processing helix chain 'a' and resid 1026 through 1031 removed outlier: 3.529A pdb=" N LEU a1030 " --> pdb=" O TYR a1026 " (cutoff:3.500A) Processing helix chain 'a' and resid 1038 through 1057 removed outlier: 3.555A pdb=" N VAL a1042 " --> pdb=" O LEU a1038 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER a1044 " --> pdb=" O ASP a1040 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR a1045 " --> pdb=" O SER a1041 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N HIS a1055 " --> pdb=" O GLN a1051 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET a1056 " --> pdb=" O GLN a1052 " (cutoff:3.500A) Processing helix chain 'a' and resid 1059 through 1073 Processing helix chain 'a' and resid 1078 through 1096 Processing helix chain 'a' and resid 1097 through 1104 Processing helix chain 'a' and resid 1110 through 1133 Processing helix chain 'a' and resid 1164 through 1176 removed outlier: 3.602A pdb=" N LEU a1176 " --> pdb=" O ILE a1172 " (cutoff:3.500A) Processing helix chain 'a' and resid 1183 through 1194 Processing helix chain 'a' and resid 1216 through 1226 removed outlier: 3.664A pdb=" N ARG a1225 " --> pdb=" O LEU a1221 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER a1226 " --> pdb=" O ARG a1222 " (cutoff:3.500A) Processing helix chain 'a' and resid 1228 through 1237 removed outlier: 3.599A pdb=" N GLN a1237 " --> pdb=" O ASP a1233 " (cutoff:3.500A) Processing helix chain 'a' and resid 1240 through 1250 Processing helix chain 'a' and resid 1254 through 1272 Processing helix chain 'a' and resid 1272 through 1280 removed outlier: 3.858A pdb=" N LEU a1276 " --> pdb=" O ASP a1272 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN a1278 " --> pdb=" O GLN a1274 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE a1280 " --> pdb=" O LEU a1276 " (cutoff:3.500A) Processing helix chain 'a' and resid 1282 through 1297 removed outlier: 3.831A pdb=" N MET a1286 " --> pdb=" O ASP a1282 " (cutoff:3.500A) Processing helix chain 'a' and resid 1301 through 1311 removed outlier: 4.257A pdb=" N SER a1311 " --> pdb=" O LEU a1307 " (cutoff:3.500A) Processing helix chain 'a' and resid 1361 through 1369 removed outlier: 3.789A pdb=" N PHE a1369 " --> pdb=" O PHE a1365 " (cutoff:3.500A) Processing helix chain 'a' and resid 1374 through 1393 Processing helix chain 'a' and resid 1402 through 1415 Processing helix chain 'a' and resid 1421 through 1428 removed outlier: 3.512A pdb=" N ARG a1427 " --> pdb=" O MET a1423 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER a1428 " --> pdb=" O SER a1424 " (cutoff:3.500A) Processing helix chain 'a' and resid 1428 through 1446 Proline residue: a1434 - end of helix removed outlier: 3.522A pdb=" N VAL a1446 " --> pdb=" O TYR a1442 " (cutoff:3.500A) Processing helix chain 'a' and resid 1451 through 1468 Processing helix chain 'a' and resid 1469 through 1473 removed outlier: 3.881A pdb=" N GLU a1473 " --> pdb=" O PRO a1470 " (cutoff:3.500A) Processing helix chain 'a' and resid 1475 through 1491 Processing helix chain 'a' and resid 1496 through 1511 Processing helix chain 'a' and resid 1513 through 1531 Processing helix chain 'a' and resid 1537 through 1552 Processing helix chain 'a' and resid 1555 through 1565 Processing helix chain 'a' and resid 1579 through 1589 removed outlier: 3.581A pdb=" N GLN a1589 " --> pdb=" O SER a1585 " (cutoff:3.500A) Processing helix chain 'a' and resid 1611 through 1613 No H-bonds generated for 'chain 'a' and resid 1611 through 1613' Processing helix chain 'a' and resid 1614 through 1626 Processing helix chain 'a' and resid 1633 through 1642 removed outlier: 3.830A pdb=" N GLN a1637 " --> pdb=" O CYS a1633 " (cutoff:3.500A) Processing helix chain 'a' and resid 1656 through 1668 Processing helix chain 'a' and resid 1669 through 1683 removed outlier: 4.637A pdb=" N LYS a1683 " --> pdb=" O VAL a1679 " (cutoff:3.500A) Processing helix chain 'a' and resid 1690 through 1703 Processing helix chain 'a' and resid 1728 through 1748 removed outlier: 3.875A pdb=" N GLN a1748 " --> pdb=" O GLU a1744 " (cutoff:3.500A) Processing helix chain 'a' and resid 1755 through 1770 Proline residue: a1763 - end of helix Processing helix chain 'a' and resid 1772 through 1791 Processing helix chain 'a' and resid 1793 through 1810 Processing helix chain 'a' and resid 1818 through 1823 removed outlier: 4.130A pdb=" N LEU a1822 " --> pdb=" O PRO a1818 " (cutoff:3.500A) Processing helix chain 'a' and resid 1825 through 1829 removed outlier: 3.837A pdb=" N ALA a1828 " --> pdb=" O GLU a1825 " (cutoff:3.500A) Processing helix chain 'a' and resid 1835 through 1848 Processing helix chain 'a' and resid 1852 through 1873 Processing helix chain 'a' and resid 1873 through 1879 removed outlier: 3.898A pdb=" N LEU a1877 " --> pdb=" O HIS a1873 " (cutoff:3.500A) Processing helix chain 'a' and resid 1880 through 1892 removed outlier: 3.580A pdb=" N ILE a1884 " --> pdb=" O HIS a1880 " (cutoff:3.500A) Processing helix chain 'a' and resid 1895 through 1902 Processing helix chain 'a' and resid 1903 through 1918 removed outlier: 3.530A pdb=" N CYS a1907 " --> pdb=" O ASN a1903 " (cutoff:3.500A) Processing helix chain 'a' and resid 1918 through 1923 removed outlier: 4.475A pdb=" N PHE a1923 " --> pdb=" O GLN a1919 " (cutoff:3.500A) Processing helix chain 'a' and resid 1927 through 1945 Processing helix chain 'a' and resid 1949 through 1951 No H-bonds generated for 'chain 'a' and resid 1949 through 1951' Processing helix chain 'a' and resid 1952 through 1970 Processing helix chain 'a' and resid 1970 through 1981 Processing helix chain 'a' and resid 1981 through 1992 removed outlier: 3.572A pdb=" N LEU a1985 " --> pdb=" O HIS a1981 " (cutoff:3.500A) Processing helix chain 'a' and resid 1995 through 2005 Processing helix chain 'a' and resid 2043 through 2047 removed outlier: 3.978A pdb=" N MET a2047 " --> pdb=" O THR a2043 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 2043 through 2047' Processing helix chain 'a' and resid 2047 through 2057 Processing helix chain 'a' and resid 2059 through 2075 removed outlier: 3.603A pdb=" N MET a2073 " --> pdb=" O ASP a2069 " (cutoff:3.500A) Processing helix chain 'a' and resid 2077 through 2083 Processing helix chain 'a' and resid 2084 through 2090 removed outlier: 3.890A pdb=" N ARG a2090 " --> pdb=" O THR a2086 " (cutoff:3.500A) Processing helix chain 'a' and resid 2091 through 2094 Processing helix chain 'a' and resid 2096 through 2114 Processing helix chain 'a' and resid 2115 through 2120 removed outlier: 3.798A pdb=" N ALA a2119 " --> pdb=" O SER a2116 " (cutoff:3.500A) Processing helix chain 'a' and resid 2121 through 2131 Processing helix chain 'a' and resid 2133 through 2143 Processing helix chain 'a' and resid 2143 through 2152 Processing helix chain 'a' and resid 2154 through 2169 Processing helix chain 'a' and resid 2173 through 2189 Processing helix chain 'b' and resid 19 through 29 Processing helix chain 'b' and resid 30 through 37 removed outlier: 3.947A pdb=" N LEU b 34 " --> pdb=" O ASP b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 45 Processing helix chain 'b' and resid 45 through 53 removed outlier: 3.502A pdb=" N ALA b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 76 Processing helix chain 'b' and resid 79 through 90 removed outlier: 4.081A pdb=" N SER b 83 " --> pdb=" O GLU b 79 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL b 90 " --> pdb=" O ALA b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 107 removed outlier: 4.297A pdb=" N LEU b 95 " --> pdb=" O ASP b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 133 Processing helix chain 'b' and resid 134 through 156 Processing helix chain 'b' and resid 175 through 188 Processing helix chain 'b' and resid 193 through 203 removed outlier: 3.526A pdb=" N LEU b 202 " --> pdb=" O ALA b 198 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS b 203 " --> pdb=" O GLU b 199 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 218 removed outlier: 4.049A pdb=" N PHE b 210 " --> pdb=" O ASN b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 231 Processing helix chain 'b' and resid 240 through 257 Processing helix chain 'b' and resid 260 through 272 Processing helix chain 'b' and resid 274 through 287 removed outlier: 4.083A pdb=" N LYS b 287 " --> pdb=" O LEU b 283 " (cutoff:3.500A) Processing helix chain 'b' and resid 296 through 308 Processing helix chain 'b' and resid 310 through 327 Processing helix chain 'b' and resid 334 through 351 removed outlier: 4.043A pdb=" N GLN b 338 " --> pdb=" O SER b 334 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 399 removed outlier: 4.362A pdb=" N LYS b 384 " --> pdb=" O GLU b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 416 Processing helix chain 'b' and resid 422 through 439 Processing helix chain 'b' and resid 439 through 444 removed outlier: 4.265A pdb=" N VAL b 443 " --> pdb=" O PHE b 439 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER b 444 " --> pdb=" O SER b 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 439 through 444' Processing helix chain 'b' and resid 445 through 462 Processing helix chain 'b' and resid 463 through 467 removed outlier: 3.706A pdb=" N GLU b 467 " --> pdb=" O ALA b 464 " (cutoff:3.500A) Processing helix chain 'b' and resid 476 through 490 Processing helix chain 'b' and resid 491 through 504 Processing helix chain 'b' and resid 510 through 525 removed outlier: 4.157A pdb=" N LEU b 514 " --> pdb=" O LYS b 510 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE b 520 " --> pdb=" O ARG b 516 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 538 Processing helix chain 'b' and resid 552 through 563 Processing helix chain 'b' and resid 564 through 570 removed outlier: 3.528A pdb=" N LYS b 568 " --> pdb=" O ARG b 564 " (cutoff:3.500A) Processing helix chain 'b' and resid 573 through 583 Processing helix chain 'b' and resid 591 through 603 Processing helix chain 'b' and resid 616 through 623 removed outlier: 3.685A pdb=" N THR b 620 " --> pdb=" O ASN b 616 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU b 623 " --> pdb=" O VAL b 619 " (cutoff:3.500A) Processing helix chain 'b' and resid 644 through 667 removed outlier: 3.850A pdb=" N LYS b 667 " --> pdb=" O LEU b 663 " (cutoff:3.500A) Processing helix chain 'b' and resid 680 through 687 removed outlier: 3.520A pdb=" N GLN b 686 " --> pdb=" O SER b 682 " (cutoff:3.500A) Processing helix chain 'b' and resid 688 through 699 Processing helix chain 'b' and resid 703 through 718 Processing helix chain 'b' and resid 719 through 722 Processing helix chain 'b' and resid 723 through 731 removed outlier: 3.875A pdb=" N TRP b 727 " --> pdb=" O ILE b 723 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU b 731 " --> pdb=" O TRP b 727 " (cutoff:3.500A) Processing helix chain 'b' and resid 735 through 745 Processing helix chain 'b' and resid 746 through 748 No H-bonds generated for 'chain 'b' and resid 746 through 748' Processing helix chain 'b' and resid 753 through 762 Processing helix chain 'b' and resid 767 through 779 removed outlier: 3.911A pdb=" N VAL b 771 " --> pdb=" O ASN b 767 " (cutoff:3.500A) Processing helix chain 'b' and resid 786 through 788 No H-bonds generated for 'chain 'b' and resid 786 through 788' Processing helix chain 'b' and resid 789 through 796 Processing helix chain 'b' and resid 797 through 802 Processing helix chain 'b' and resid 806 through 824 removed outlier: 3.738A pdb=" N LEU b 810 " --> pdb=" O PRO b 806 " (cutoff:3.500A) Processing helix chain 'b' and resid 824 through 836 Processing helix chain 'b' and resid 849 through 856 Processing helix chain 'b' and resid 857 through 862 Processing helix chain 'b' and resid 864 through 869 Processing helix chain 'b' and resid 870 through 899 Processing helix chain 'b' and resid 923 through 947 Processing helix chain 'b' and resid 949 through 954 Processing helix chain 'b' and resid 988 through 1008 Processing helix chain 'b' and resid 1008 through 1019 removed outlier: 3.983A pdb=" N ALA b1012 " --> pdb=" O ASP b1008 " (cutoff:3.500A) Processing helix chain 'b' and resid 1021 through 1023 No H-bonds generated for 'chain 'b' and resid 1021 through 1023' Processing helix chain 'b' and resid 1024 through 1032 Processing helix chain 'b' and resid 1033 through 1036 removed outlier: 3.850A pdb=" N HIS b1036 " --> pdb=" O PRO b1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1033 through 1036' Processing helix chain 'b' and resid 1037 through 1047 removed outlier: 4.182A pdb=" N PHE b1041 " --> pdb=" O ILE b1037 " (cutoff:3.500A) Proline residue: b1043 - end of helix Processing helix chain 'b' and resid 1050 through 1068 Processing helix chain 'b' and resid 1070 through 1088 Processing helix chain 'b' and resid 1092 through 1104 Proline residue: b1102 - end of helix Processing helix chain 'b' and resid 1104 through 1114 removed outlier: 4.137A pdb=" N VAL b1108 " --> pdb=" O LEU b1104 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER b1109 " --> pdb=" O PRO b1105 " (cutoff:3.500A) Processing helix chain 'b' and resid 1117 through 1139 removed outlier: 3.923A pdb=" N GLN b1139 " --> pdb=" O ASP b1135 " (cutoff:3.500A) Processing helix chain 'b' and resid 1180 through 1202 Processing helix chain 'c' and resid 46 through 64 removed outlier: 3.514A pdb=" N THR c 63 " --> pdb=" O VAL c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 82 removed outlier: 4.186A pdb=" N GLY c 82 " --> pdb=" O TYR c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 98 Processing helix chain 'c' and resid 100 through 115 Processing helix chain 'c' and resid 119 through 134 Processing helix chain 'c' and resid 135 through 137 No H-bonds generated for 'chain 'c' and resid 135 through 137' Processing helix chain 'c' and resid 138 through 156 Processing helix chain 'c' and resid 159 through 170 removed outlier: 3.659A pdb=" N VAL c 163 " --> pdb=" O GLY c 159 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN c 170 " --> pdb=" O THR c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 194 Processing helix chain 'c' and resid 194 through 200 Processing helix chain 'c' and resid 201 through 219 removed outlier: 3.918A pdb=" N ALA c 206 " --> pdb=" O SER c 202 " (cutoff:3.500A) Processing helix chain 'c' and resid 222 through 243 Processing helix chain 'c' and resid 243 through 248 Processing helix chain 'c' and resid 249 through 251 No H-bonds generated for 'chain 'c' and resid 249 through 251' Processing helix chain 'c' and resid 252 through 261 removed outlier: 3.834A pdb=" N ASN c 260 " --> pdb=" O ARG c 256 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL c 261 " --> pdb=" O LEU c 257 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 277 Processing helix chain 'c' and resid 277 through 282 removed outlier: 4.250A pdb=" N LEU c 281 " --> pdb=" O ASN c 277 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER c 282 " --> pdb=" O PRO c 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 277 through 282' Processing helix chain 'c' and resid 287 through 294 removed outlier: 4.319A pdb=" N LEU c 291 " --> pdb=" O GLY c 287 " (cutoff:3.500A) Processing helix chain 'c' and resid 297 through 304 removed outlier: 4.087A pdb=" N LEU c 301 " --> pdb=" O SER c 297 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG c 304 " --> pdb=" O PHE c 300 " (cutoff:3.500A) Processing helix chain 'c' and resid 306 through 319 removed outlier: 3.587A pdb=" N GLU c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 324 through 336 removed outlier: 4.331A pdb=" N TYR c 328 " --> pdb=" O GLN c 324 " (cutoff:3.500A) Processing helix chain 'c' and resid 341 through 356 Processing helix chain 'c' and resid 360 through 366 Processing helix chain 'c' and resid 370 through 381 removed outlier: 4.136A pdb=" N ILE c 374 " --> pdb=" O PRO c 370 " (cutoff:3.500A) Processing helix chain 'c' and resid 384 through 398 removed outlier: 4.487A pdb=" N ASP c 398 " --> pdb=" O ALA c 394 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 402 removed outlier: 4.161A pdb=" N PHE c 402 " --> pdb=" O TRP c 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 399 through 402' Processing helix chain 'c' and resid 408 through 411 removed outlier: 3.695A pdb=" N ASN c 411 " --> pdb=" O SER c 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 408 through 411' Processing helix chain 'c' and resid 412 through 422 Processing helix chain 'c' and resid 426 through 445 removed outlier: 3.799A pdb=" N THR c 430 " --> pdb=" O HIS c 426 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE c 441 " --> pdb=" O MET c 437 " (cutoff:3.500A) Proline residue: c 442 - end of helix removed outlier: 4.714A pdb=" N TYR c 445 " --> pdb=" O ILE c 441 " (cutoff:3.500A) Processing helix chain 'c' and resid 448 through 466 removed outlier: 3.510A pdb=" N VAL c 452 " --> pdb=" O LEU c 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 472 through 477 removed outlier: 3.561A pdb=" N ASP c 477 " --> pdb=" O ALA c 473 " (cutoff:3.500A) Processing helix chain 'c' and resid 482 through 493 removed outlier: 3.634A pdb=" N ARG c 486 " --> pdb=" O ASP c 482 " (cutoff:3.500A) Processing helix chain 'c' and resid 494 through 497 Processing helix chain 'd' and resid 36 through 46 Processing helix chain 'd' and resid 50 through 62 removed outlier: 3.536A pdb=" N GLN d 54 " --> pdb=" O ALA d 50 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS d 62 " --> pdb=" O GLN d 58 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 83 removed outlier: 4.106A pdb=" N ARG d 74 " --> pdb=" O GLU d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 101 Processing helix chain 'd' and resid 108 through 121 removed outlier: 3.588A pdb=" N ASP d 112 " --> pdb=" O ASP d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 141 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 163 through 177 Processing helix chain 'd' and resid 196 through 203 Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 208 through 226 Processing helix chain 'd' and resid 232 through 241 Processing helix chain 'd' and resid 245 through 252 removed outlier: 3.792A pdb=" N ARG d 249 " --> pdb=" O TYR d 245 " (cutoff:3.500A) Processing helix chain 'd' and resid 255 through 263 Processing helix chain 'd' and resid 279 through 292 removed outlier: 4.088A pdb=" N SER d 292 " --> pdb=" O CYS d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 295 through 308 Processing helix chain 'd' and resid 313 through 322 removed outlier: 3.657A pdb=" N LEU d 317 " --> pdb=" O SER d 313 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP d 322 " --> pdb=" O GLU d 318 " (cutoff:3.500A) Processing helix chain 'd' and resid 377 through 384 Processing helix chain 'd' and resid 387 through 405 Processing helix chain 'd' and resid 405 through 420 removed outlier: 3.552A pdb=" N ALA d 409 " --> pdb=" O SER d 405 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP d 414 " --> pdb=" O GLU d 410 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE d 415 " --> pdb=" O LYS d 411 " (cutoff:3.500A) Processing helix chain 'd' and resid 424 through 438 Processing helix chain 'd' and resid 445 through 457 removed outlier: 3.657A pdb=" N GLU d 457 " --> pdb=" O LEU d 453 " (cutoff:3.500A) Processing helix chain 'd' and resid 460 through 474 removed outlier: 3.963A pdb=" N CYS d 473 " --> pdb=" O GLU d 469 " (cutoff:3.500A) Processing helix chain 'd' and resid 478 through 496 removed outlier: 3.565A pdb=" N ILE d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 499 through 514 Processing helix chain 'd' and resid 514 through 519 removed outlier: 3.570A pdb=" N VAL d 518 " --> pdb=" O HIS d 514 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU d 519 " --> pdb=" O PRO d 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 514 through 519' Processing helix chain 'd' and resid 521 through 526 Processing helix chain 'd' and resid 541 through 555 Processing helix chain 'd' and resid 560 through 565 removed outlier: 3.647A pdb=" N ALA d 563 " --> pdb=" O THR d 560 " (cutoff:3.500A) Processing helix chain 'd' and resid 566 through 580 Processing helix chain 'd' and resid 609 through 624 Processing helix chain 'd' and resid 628 through 650 Processing helix chain 'd' and resid 653 through 674 Processing helix chain 'd' and resid 675 through 681 removed outlier: 6.256A pdb=" N LEU d 678 " --> pdb=" O GLN d 675 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP d 679 " --> pdb=" O GLU d 676 " (cutoff:3.500A) Processing helix chain 'd' and resid 692 through 710 Processing helix chain 'd' and resid 715 through 741 removed outlier: 4.281A pdb=" N ILE d 721 " --> pdb=" O LYS d 717 " (cutoff:3.500A) Processing helix chain 'd' and resid 743 through 765 removed outlier: 3.574A pdb=" N LEU d 747 " --> pdb=" O GLY d 743 " (cutoff:3.500A) Processing helix chain 'd' and resid 766 through 772 removed outlier: 3.909A pdb=" N LEU d 769 " --> pdb=" O ILE d 766 " (cutoff:3.500A) Proline residue: d 770 - end of helix No H-bonds generated for 'chain 'd' and resid 766 through 772' Processing helix chain 'd' and resid 775 through 783 Processing helix chain 'd' and resid 783 through 790 Processing helix chain 'd' and resid 791 through 805 removed outlier: 3.717A pdb=" N GLN d 805 " --> pdb=" O THR d 801 " (cutoff:3.500A) Processing helix chain 'd' and resid 856 through 860 Processing helix chain 'e' and resid 27 through 41 removed outlier: 3.708A pdb=" N LEU e 31 " --> pdb=" O SER e 27 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 64 Processing helix chain 'e' and resid 66 through 95 removed outlier: 3.868A pdb=" N GLY e 79 " --> pdb=" O ASP e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 117 through 136 removed outlier: 3.597A pdb=" N VAL e 122 " --> pdb=" O LEU e 118 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN e 136 " --> pdb=" O PHE e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 163 removed outlier: 3.565A pdb=" N TRP e 140 " --> pdb=" O ASN e 136 " (cutoff:3.500A) Proline residue: e 142 - end of helix removed outlier: 5.189A pdb=" N GLY e 161 " --> pdb=" O SER e 157 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN e 162 " --> pdb=" O THR e 158 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS e 163 " --> pdb=" O TYR e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 183 removed outlier: 4.031A pdb=" N CYS e 183 " --> pdb=" O LEU e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 204 removed outlier: 4.564A pdb=" N GLY e 202 " --> pdb=" O SER e 198 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER e 203 " --> pdb=" O ALA e 199 " (cutoff:3.500A) Processing helix chain 'e' and resid 204 through 219 Processing helix chain 'e' and resid 219 through 234 removed outlier: 3.982A pdb=" N PHE e 223 " --> pdb=" O HIS e 219 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP e 224 " --> pdb=" O SER e 220 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TRP e 225 " --> pdb=" O PRO e 221 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL e 226 " --> pdb=" O HIS e 222 " (cutoff:3.500A) Processing helix chain 'e' and resid 234 through 254 removed outlier: 3.949A pdb=" N ILE e 238 " --> pdb=" O PHE e 234 " (cutoff:3.500A) Processing helix chain 'e' and resid 291 through 304 removed outlier: 4.026A pdb=" N ARG e 304 " --> pdb=" O HIS e 300 " (cutoff:3.500A) Processing helix chain 'e' and resid 306 through 320 removed outlier: 3.819A pdb=" N SER e 320 " --> pdb=" O MET e 316 " (cutoff:3.500A) Processing helix chain 'e' and resid 339 through 348 Processing helix chain 'e' and resid 348 through 362 Processing helix chain 'e' and resid 367 through 377 Processing helix chain 'e' and resid 380 through 399 removed outlier: 3.979A pdb=" N SER e 399 " --> pdb=" O VAL e 395 " (cutoff:3.500A) Processing helix chain 'e' and resid 402 through 414 Processing helix chain 'e' and resid 429 through 451 Processing helix chain 'e' and resid 471 through 480 removed outlier: 4.297A pdb=" N ASN e 479 " --> pdb=" O ASP e 475 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS e 480 " --> pdb=" O ALA e 476 " (cutoff:3.500A) Processing helix chain 'e' and resid 480 through 490 removed outlier: 3.535A pdb=" N LEU e 484 " --> pdb=" O HIS e 480 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG e 490 " --> pdb=" O GLY e 486 " (cutoff:3.500A) Processing helix chain 'e' and resid 494 through 510 removed outlier: 3.922A pdb=" N TRP e 498 " --> pdb=" O LYS e 494 " (cutoff:3.500A) Processing helix chain 'e' and resid 514 through 526 Processing helix chain 'e' and resid 528 through 544 removed outlier: 4.171A pdb=" N VAL e 544 " --> pdb=" O ALA e 540 " (cutoff:3.500A) Processing helix chain 'e' and resid 548 through 563 removed outlier: 3.947A pdb=" N LEU e 552 " --> pdb=" O GLY e 548 " (cutoff:3.500A) Processing helix chain 'e' and resid 567 through 587 Processing helix chain 'e' and resid 589 through 596 removed outlier: 3.926A pdb=" N ALA e 593 " --> pdb=" O GLY e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 598 through 606 removed outlier: 3.773A pdb=" N HIS e 606 " --> pdb=" O SER e 602 " (cutoff:3.500A) Processing helix chain 'e' and resid 606 through 611 Processing helix chain 'e' and resid 612 through 616 Processing helix chain 'e' and resid 618 through 632 Processing helix chain 'e' and resid 640 through 663 Processing helix chain 'e' and resid 664 through 666 No H-bonds generated for 'chain 'e' and resid 664 through 666' Processing helix chain 'e' and resid 667 through 681 removed outlier: 4.222A pdb=" N SER e 681 " --> pdb=" O LEU e 677 " (cutoff:3.500A) Processing helix chain 'e' and resid 681 through 698 Processing helix chain 'e' and resid 701 through 706 removed outlier: 3.567A pdb=" N GLY e 706 " --> pdb=" O GLU e 703 " (cutoff:3.500A) Processing helix chain 'e' and resid 727 through 735 Processing helix chain 'e' and resid 768 through 788 Processing helix chain 'e' and resid 805 through 821 Processing helix chain 'e' and resid 833 through 840 Processing helix chain 'e' and resid 840 through 854 Processing helix chain 'e' and resid 855 through 867 removed outlier: 3.971A pdb=" N GLU e 859 " --> pdb=" O PRO e 855 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA e 867 " --> pdb=" O LEU e 863 " (cutoff:3.500A) Processing helix chain 'e' and resid 868 through 873 removed outlier: 3.646A pdb=" N LEU e 871 " --> pdb=" O PRO e 868 " (cutoff:3.500A) Processing helix chain 'e' and resid 874 through 892 Processing helix chain 'e' and resid 896 through 899 removed outlier: 3.927A pdb=" N HIS e 899 " --> pdb=" O ASP e 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 896 through 899' Processing helix chain 'e' and resid 900 through 917 Processing helix chain 'e' and resid 921 through 926 Processing helix chain 'e' and resid 927 through 930 Processing helix chain 'e' and resid 935 through 953 Processing helix chain 'e' and resid 956 through 958 No H-bonds generated for 'chain 'e' and resid 956 through 958' Processing helix chain 'e' and resid 981 through 995 Processing helix chain 'e' and resid 995 through 1000 Processing helix chain 'e' and resid 1001 through 1007 removed outlier: 4.007A pdb=" N GLY e1004 " --> pdb=" O LEU e1001 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE e1006 " --> pdb=" O SER e1003 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 16 Processing helix chain 'f' and resid 23 through 40 Processing helix chain 'f' and resid 41 through 48 removed outlier: 6.312A pdb=" N ALA f 44 " --> pdb=" O ARG f 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG f 46 " --> pdb=" O PRO f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 57 through 61 Processing helix chain 'f' and resid 69 through 79 Processing helix chain 'f' and resid 87 through 100 Processing helix chain 'f' and resid 102 through 107 Processing helix chain 'f' and resid 154 through 158 Processing helix chain 'f' and resid 182 through 187 Processing helix chain 'f' and resid 195 through 203 removed outlier: 4.569A pdb=" N MET f 199 " --> pdb=" O ALA f 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR f 203 " --> pdb=" O MET f 199 " (cutoff:3.500A) Processing helix chain 'f' and resid 212 through 226 Processing helix chain 'f' and resid 259 through 263 Processing helix chain 'f' and resid 332 through 340 Processing helix chain 'f' and resid 385 through 400 removed outlier: 3.549A pdb=" N LEU f 389 " --> pdb=" O ASN f 385 " (cutoff:3.500A) Proline residue: f 391 - end of helix Processing helix chain 'f' and resid 405 through 418 removed outlier: 3.534A pdb=" N THR f 418 " --> pdb=" O SER f 414 " (cutoff:3.500A) Processing helix chain 'f' and resid 419 through 422 removed outlier: 6.080A pdb=" N TYR f 422 " --> pdb=" O MET f 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 419 through 422' Processing helix chain 'f' and resid 423 through 435 Processing helix chain 'f' and resid 439 through 444 Processing helix chain 'f' and resid 449 through 474 Processing helix chain 'f' and resid 543 through 547 removed outlier: 3.717A pdb=" N ASP f 546 " --> pdb=" O ASN f 543 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE f 547 " --> pdb=" O ALA f 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 543 through 547' Processing helix chain 'f' and resid 548 through 550 No H-bonds generated for 'chain 'f' and resid 548 through 550' Processing helix chain 'f' and resid 551 through 564 Processing helix chain 'f' and resid 589 through 597 removed outlier: 3.594A pdb=" N TYR f 593 " --> pdb=" O ASN f 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 34 removed outlier: 4.225A pdb=" N GLY g 32 " --> pdb=" O GLU g 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU g 33 " --> pdb=" O LEU g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 55 Proline residue: g 49 - end of helix Processing helix chain 'g' and resid 57 through 75 Processing helix chain 'g' and resid 76 through 90 Processing helix chain 'g' and resid 93 through 97 Processing helix chain 'g' and resid 99 through 109 Processing helix chain 'g' and resid 110 through 113 Processing helix chain 'g' and resid 115 through 129 Processing helix chain 'g' and resid 130 through 132 No H-bonds generated for 'chain 'g' and resid 130 through 132' Processing helix chain 'g' and resid 136 through 147 Processing helix chain 'g' and resid 151 through 169 Processing helix chain 'g' and resid 170 through 185 Processing helix chain 'g' and resid 190 through 198 Processing helix chain 'g' and resid 199 through 204 Processing helix chain 'g' and resid 207 through 225 Processing helix chain 'g' and resid 227 through 245 Processing helix chain 'g' and resid 248 through 263 Processing helix chain 'g' and resid 265 through 283 Processing helix chain 'g' and resid 284 through 287 Processing helix chain 'g' and resid 288 through 302 Processing helix chain 'g' and resid 304 through 320 Processing helix chain 'g' and resid 322 through 328 Processing helix chain 'g' and resid 342 through 353 removed outlier: 3.898A pdb=" N TYR g 353 " --> pdb=" O GLN g 349 " (cutoff:3.500A) Processing helix chain 'g' and resid 356 through 374 removed outlier: 3.713A pdb=" N CYS g 374 " --> pdb=" O ILE g 370 " (cutoff:3.500A) Processing helix chain 'g' and resid 376 through 398 removed outlier: 4.869A pdb=" N GLN g 384 " --> pdb=" O LEU g 380 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP g 385 " --> pdb=" O ALA g 381 " (cutoff:3.500A) Processing helix chain 'g' and resid 402 through 423 Processing helix chain 'g' and resid 423 through 441 removed outlier: 4.309A pdb=" N SER g 429 " --> pdb=" O HIS g 425 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS g 439 " --> pdb=" O LEU g 435 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER g 440 " --> pdb=" O THR g 436 " (cutoff:3.500A) Processing helix chain 'g' and resid 442 through 460 Processing helix chain 'g' and resid 465 through 479 removed outlier: 3.962A pdb=" N GLY g 469 " --> pdb=" O ASP g 465 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP g 470 " --> pdb=" O GLY g 466 " (cutoff:3.500A) Processing helix chain 'g' and resid 485 through 501 removed outlier: 3.576A pdb=" N LEU g 489 " --> pdb=" O LYS g 485 " (cutoff:3.500A) Processing helix chain 'g' and resid 506 through 520 removed outlier: 3.874A pdb=" N LYS g 510 " --> pdb=" O SER g 506 " (cutoff:3.500A) Processing helix chain 'g' and resid 523 through 537 Processing helix chain 'g' and resid 538 through 550 Processing helix chain 'g' and resid 555 through 576 removed outlier: 3.596A pdb=" N TYR g 559 " --> pdb=" O SER g 555 " (cutoff:3.500A) Processing helix chain 'g' and resid 583 through 608 Processing helix chain 'g' and resid 614 through 644 removed outlier: 4.326A pdb=" N LYS g 642 " --> pdb=" O CYS g 638 " (cutoff:3.500A) Processing helix chain 'g' and resid 664 through 692 Processing helix chain 'g' and resid 696 through 721 Processing helix chain 'g' and resid 734 through 738 Processing helix chain 'g' and resid 742 through 762 removed outlier: 3.540A pdb=" N LEU g 762 " --> pdb=" O GLU g 758 " (cutoff:3.500A) Processing helix chain 'g' and resid 770 through 787 removed outlier: 3.773A pdb=" N THR g 774 " --> pdb=" O SER g 770 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL g 787 " --> pdb=" O ALA g 783 " (cutoff:3.500A) Processing helix chain 'g' and resid 792 through 797 removed outlier: 3.837A pdb=" N PHE g 796 " --> pdb=" O GLN g 792 " (cutoff:3.500A) Processing helix chain 'g' and resid 933 through 944 Processing helix chain 'h' and resid 25 through 30 removed outlier: 4.229A pdb=" N LEU h 29 " --> pdb=" O PHE h 25 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU h 30 " --> pdb=" O GLU h 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 25 through 30' Processing helix chain 'h' and resid 48 through 60 Processing helix chain 'h' and resid 76 through 92 removed outlier: 3.539A pdb=" N LEU h 92 " --> pdb=" O VAL h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 103 Processing helix chain 'h' and resid 104 through 120 Processing helix chain 'h' and resid 127 through 131 Processing helix chain 'h' and resid 136 through 159 Processing helix chain 'h' and resid 177 through 194 Processing helix chain 'h' and resid 194 through 208 Processing helix chain 'h' and resid 244 through 264 removed outlier: 3.500A pdb=" N MET h 248 " --> pdb=" O LYS h 244 " (cutoff:3.500A) Processing helix chain 'h' and resid 267 through 289 Processing helix chain 'h' and resid 298 through 313 Processing helix chain 'h' and resid 324 through 336 Processing helix chain 'h' and resid 337 through 352 Processing helix chain 'h' and resid 355 through 373 Processing helix chain 'h' and resid 376 through 396 removed outlier: 3.921A pdb=" N ILE h 380 " --> pdb=" O ALA h 376 " (cutoff:3.500A) Processing helix chain 'h' and resid 400 through 407 Processing helix chain 'h' and resid 411 through 427 removed outlier: 4.176A pdb=" N ASN h 427 " --> pdb=" O SER h 423 " (cutoff:3.500A) Processing helix chain 'h' and resid 432 through 450 removed outlier: 3.515A pdb=" N LYS h 436 " --> pdb=" O SER h 432 " (cutoff:3.500A) Processing helix chain 'h' and resid 452 through 462 removed outlier: 3.620A pdb=" N HIS h 462 " --> pdb=" O MET h 458 " (cutoff:3.500A) Processing helix chain 'h' and resid 462 through 469 Processing helix chain 'h' and resid 470 through 483 Processing helix chain 'h' and resid 504 through 519 removed outlier: 3.636A pdb=" N ASN h 508 " --> pdb=" O SER h 504 " (cutoff:3.500A) Processing helix chain 'h' and resid 521 through 536 Processing helix chain 'h' and resid 540 through 544 Processing helix chain 'h' and resid 551 through 559 removed outlier: 4.105A pdb=" N VAL h 557 " --> pdb=" O VAL h 553 " (cutoff:3.500A) Processing helix chain 'h' and resid 563 through 583 Processing helix chain 'h' and resid 585 through 601 Processing helix chain 'h' and resid 604 through 626 removed outlier: 3.505A pdb=" N ARG h 608 " --> pdb=" O SER h 604 " (cutoff:3.500A) Processing helix chain 'h' and resid 637 through 648 Processing helix chain 'h' and resid 656 through 670 removed outlier: 3.909A pdb=" N ALA h 660 " --> pdb=" O ARG h 656 " (cutoff:3.500A) Processing helix chain 'h' and resid 672 through 679 Processing helix chain 'h' and resid 681 through 688 Processing helix chain 'h' and resid 688 through 703 removed outlier: 3.786A pdb=" N LYS h 692 " --> pdb=" O ASN h 688 " (cutoff:3.500A) Processing helix chain 'h' and resid 706 through 726 Processing helix chain 'h' and resid 740 through 745 removed outlier: 3.879A pdb=" N GLN h 744 " --> pdb=" O SER h 740 " (cutoff:3.500A) Processing helix chain 'h' and resid 753 through 763 Processing helix chain 'h' and resid 766 through 784 removed outlier: 4.064A pdb=" N ARG h 784 " --> pdb=" O LEU h 780 " (cutoff:3.500A) Processing helix chain 'h' and resid 795 through 799 removed outlier: 3.670A pdb=" N ILE h 798 " --> pdb=" O HIS h 795 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP h 799 " --> pdb=" O ILE h 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 795 through 799' Processing helix chain 'h' and resid 805 through 809 Processing helix chain 'h' and resid 810 through 829 Processing helix chain 'h' and resid 832 through 846 Processing helix chain 'h' and resid 848 through 864 Processing helix chain 'h' and resid 877 through 891 Processing helix chain 'h' and resid 893 through 901 Processing helix chain 'h' and resid 902 through 904 No H-bonds generated for 'chain 'h' and resid 902 through 904' Processing helix chain 'h' and resid 908 through 917 Processing helix chain 'h' and resid 925 through 931 removed outlier: 3.878A pdb=" N ASP h 930 " --> pdb=" O SER h 927 " (cutoff:3.500A) Processing helix chain 'h' and resid 934 through 949 removed outlier: 3.583A pdb=" N LEU h 938 " --> pdb=" O ASP h 934 " (cutoff:3.500A) Processing helix chain 'h' and resid 950 through 962 Processing helix chain 'h' and resid 971 through 995 Processing helix chain 'i' and resid 31 through 38 removed outlier: 4.005A pdb=" N SER i 34 " --> pdb=" O ASP i 31 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 51 removed outlier: 3.554A pdb=" N SER i 50 " --> pdb=" O SER i 46 " (cutoff:3.500A) Processing helix chain 'i' and resid 87 through 91 removed outlier: 3.650A pdb=" N LEU i 90 " --> pdb=" O GLU i 87 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE i 91 " --> pdb=" O THR i 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 87 through 91' Processing helix chain 'i' and resid 109 through 116 removed outlier: 3.650A pdb=" N ILE i 113 " --> pdb=" O ALA i 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 147 removed outlier: 4.537A pdb=" N VAL i 147 " --> pdb=" O PHE i 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 154 through 157 Processing helix chain 'i' and resid 158 through 165 Processing helix chain 'i' and resid 166 through 171 Processing helix chain 'i' and resid 174 through 176 No H-bonds generated for 'chain 'i' and resid 174 through 176' Processing helix chain 'i' and resid 183 through 193 removed outlier: 4.152A pdb=" N LYS i 193 " --> pdb=" O SER i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 252 through 256 removed outlier: 3.536A pdb=" N LEU i 255 " --> pdb=" O GLN i 252 " (cutoff:3.500A) Processing helix chain 'i' and resid 273 through 292 Processing helix chain 'i' and resid 302 through 320 removed outlier: 3.623A pdb=" N TYR i 306 " --> pdb=" O SER i 302 " (cutoff:3.500A) Processing helix chain 'i' and resid 332 through 343 Processing helix chain 'i' and resid 348 through 357 removed outlier: 3.727A pdb=" N LEU i 357 " --> pdb=" O SER i 353 " (cutoff:3.500A) Processing helix chain 'i' and resid 363 through 370 removed outlier: 3.530A pdb=" N LEU i 367 " --> pdb=" O PRO i 363 " (cutoff:3.500A) Processing helix chain 'i' and resid 382 through 387 Processing helix chain 'i' and resid 403 through 413 removed outlier: 4.310A pdb=" N HIS i 407 " --> pdb=" O GLY i 403 " (cutoff:3.500A) Processing helix chain 'i' and resid 428 through 434 Processing helix chain 'i' and resid 453 through 465 Processing helix chain 'i' and resid 473 through 477 Processing helix chain 'i' and resid 519 through 525 removed outlier: 3.692A pdb=" N ALA i 523 " --> pdb=" O MET i 519 " (cutoff:3.500A) Processing helix chain 'i' and resid 590 through 602 removed outlier: 3.755A pdb=" N GLY i 602 " --> pdb=" O LEU i 598 " (cutoff:3.500A) Processing helix chain 'i' and resid 640 through 654 removed outlier: 3.844A pdb=" N PHE i 654 " --> pdb=" O LEU i 650 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 17 Processing helix chain 'j' and resid 21 through 33 removed outlier: 3.554A pdb=" N ALA j 25 " --> pdb=" O ASP j 21 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG j 33 " --> pdb=" O LEU j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 35 through 47 Processing helix chain 'j' and resid 52 through 70 Processing helix chain 'j' and resid 73 through 88 removed outlier: 4.150A pdb=" N TRP j 77 " --> pdb=" O GLN j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 105 removed outlier: 4.116A pdb=" N GLN j 97 " --> pdb=" O ASP j 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 107 through 122 removed outlier: 3.570A pdb=" N GLN j 111 " --> pdb=" O PRO j 107 " (cutoff:3.500A) Processing helix chain 'j' and resid 124 through 139 removed outlier: 3.636A pdb=" N PHE j 139 " --> pdb=" O LEU j 135 " (cutoff:3.500A) Processing helix chain 'j' and resid 139 through 147 removed outlier: 4.093A pdb=" N VAL j 143 " --> pdb=" O PHE j 139 " (cutoff:3.500A) Processing helix chain 'j' and resid 148 through 161 removed outlier: 4.036A pdb=" N GLU j 152 " --> pdb=" O VAL j 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 185 Proline residue: j 180 - end of helix removed outlier: 3.516A pdb=" N ASN j 185 " --> pdb=" O LEU j 181 " (cutoff:3.500A) Processing helix chain 'j' and resid 191 through 211 Processing helix chain 'j' and resid 246 through 250 Processing helix chain 'j' and resid 254 through 270 removed outlier: 3.564A pdb=" N CYS j 270 " --> pdb=" O VAL j 266 " (cutoff:3.500A) Processing helix chain 'j' and resid 283 through 298 removed outlier: 3.726A pdb=" N ASN j 297 " --> pdb=" O ARG j 293 " (cutoff:3.500A) Processing helix chain 'j' and resid 300 through 330 Processing helix chain 'j' and resid 351 through 356 Processing helix chain 'j' and resid 366 through 375 Processing helix chain 'j' and resid 405 through 424 Processing helix chain 'j' and resid 426 through 441 removed outlier: 3.770A pdb=" N LYS j 441 " --> pdb=" O CYS j 437 " (cutoff:3.500A) Processing helix chain 'j' and resid 445 through 460 Processing helix chain 'j' and resid 461 through 479 removed outlier: 3.733A pdb=" N ALA j 465 " --> pdb=" O GLN j 461 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE j 479 " --> pdb=" O LEU j 475 " (cutoff:3.500A) Processing helix chain 'j' and resid 492 through 506 Processing helix chain 'j' and resid 508 through 522 Processing helix chain 'j' and resid 556 through 578 removed outlier: 3.788A pdb=" N ILE j 560 " --> pdb=" O THR j 556 " (cutoff:3.500A) Proline residue: j 562 - end of helix removed outlier: 4.521A pdb=" N LEU j 565 " --> pdb=" O MET j 561 " (cutoff:3.500A) Processing helix chain 'j' and resid 582 through 592 Processing helix chain 'j' and resid 598 through 612 Processing helix chain 'j' and resid 621 through 626 removed outlier: 3.534A pdb=" N VAL j 626 " --> pdb=" O PHE j 622 " (cutoff:3.500A) Processing helix chain 'j' and resid 628 through 640 removed outlier: 3.630A pdb=" N LEU j 632 " --> pdb=" O ASN j 628 " (cutoff:3.500A) Processing helix chain 'j' and resid 653 through 660 removed outlier: 3.600A pdb=" N LEU j 657 " --> pdb=" O ASN j 653 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS j 660 " --> pdb=" O MET j 656 " (cutoff:3.500A) Processing helix chain 'j' and resid 664 through 685 Processing helix chain 'j' and resid 689 through 706 removed outlier: 4.065A pdb=" N VAL j 693 " --> pdb=" O ASN j 689 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU j 706 " --> pdb=" O LYS j 702 " (cutoff:3.500A) Processing helix chain 'j' and resid 707 through 709 No H-bonds generated for 'chain 'j' and resid 707 through 709' Processing helix chain 'k' and resid 47 through 51 Processing helix chain 'k' and resid 56 through 60 removed outlier: 3.952A pdb=" N PHE k 60 " --> pdb=" O ARG k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 60' Processing helix chain 'k' and resid 70 through 75 Processing helix chain 'k' and resid 76 through 82 Processing helix chain 'k' and resid 94 through 114 Proline residue: k 101 - end of helix Processing helix chain 'k' and resid 122 through 133 Processing helix chain 'k' and resid 214 through 232 Processing helix chain 'k' and resid 241 through 260 Processing helix chain 'k' and resid 269 through 282 removed outlier: 3.653A pdb=" N GLU k 273 " --> pdb=" O THR k 269 " (cutoff:3.500A) Processing helix chain 'k' and resid 283 through 286 Processing helix chain 'k' and resid 287 through 297 removed outlier: 4.142A pdb=" N VAL k 295 " --> pdb=" O ARG k 291 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN k 296 " --> pdb=" O LYS k 292 " (cutoff:3.500A) Processing helix chain 'k' and resid 335 through 340 Processing helix chain 'k' and resid 394 through 406 removed outlier: 3.547A pdb=" N ILE k 398 " --> pdb=" O ASP k 394 " (cutoff:3.500A) Processing helix chain 'k' and resid 416 through 432 Processing helix chain 'k' and resid 458 through 470 Processing helix chain 'k' and resid 494 through 499 Processing helix chain 'k' and resid 500 through 502 No H-bonds generated for 'chain 'k' and resid 500 through 502' Processing helix chain 'k' and resid 523 through 538 Processing helix chain 'k' and resid 577 through 594 removed outlier: 3.816A pdb=" N LEU k 583 " --> pdb=" O GLN k 579 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY k 594 " --> pdb=" O LEU k 590 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 15 Processing helix chain 'n' and resid 26 through 34 Processing helix chain 'n' and resid 35 through 46 Processing helix chain 'n' and resid 69 through 78 removed outlier: 3.784A pdb=" N LEU n 73 " --> pdb=" O ASP n 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER n 78 " --> pdb=" O GLN n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 88 through 104 Processing helix chain 'n' and resid 126 through 132 removed outlier: 4.223A pdb=" N LEU n 130 " --> pdb=" O LEU n 126 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA n 131 " --> pdb=" O ARG n 127 " (cutoff:3.500A) Processing helix chain 'n' and resid 159 through 167 Processing helix chain 'n' and resid 167 through 179 removed outlier: 3.738A pdb=" N ASN n 179 " --> pdb=" O LEU n 175 " (cutoff:3.500A) Processing helix chain 'n' and resid 195 through 205 Processing helix chain 'o' and resid 2 through 10 removed outlier: 3.763A pdb=" N ARG o 10 " --> pdb=" O HIS o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 31 Processing helix chain 'o' and resid 42 through 52 Processing helix chain 'o' and resid 68 through 86 removed outlier: 3.545A pdb=" N LEU o 72 " --> pdb=" O SER o 68 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN o 73 " --> pdb=" O LEU o 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 Processing helix chain 'o' and resid 104 through 125 removed outlier: 4.260A pdb=" N ASP o 108 " --> pdb=" O ASN o 104 " (cutoff:3.500A) Processing helix chain 'o' and resid 126 through 139 Processing helix chain 'o' and resid 141 through 159 Processing helix chain 'o' and resid 163 through 174 Processing helix chain 'o' and resid 174 through 189 Processing helix chain 'o' and resid 193 through 197 Processing helix chain 'o' and resid 199 through 224 removed outlier: 3.582A pdb=" N GLU o 212 " --> pdb=" O THR o 208 " (cutoff:3.500A) Proline residue: o 214 - end of helix Processing helix chain 'o' and resid 239 through 257 Proline residue: o 251 - end of helix Processing helix chain 'o' and resid 281 through 306 Processing helix chain 'o' and resid 321 through 335 removed outlier: 4.081A pdb=" N GLU o 335 " --> pdb=" O ARG o 331 " (cutoff:3.500A) Processing helix chain 'o' and resid 341 through 362 Processing helix chain 'o' and resid 369 through 379 Processing helix chain 'o' and resid 383 through 390 removed outlier: 3.724A pdb=" N LEU o 387 " --> pdb=" O ASN o 383 " (cutoff:3.500A) Processing helix chain 'p' and resid 11 through 23 removed outlier: 4.161A pdb=" N VAL p 15 " --> pdb=" O TYR p 11 " (cutoff:3.500A) Processing helix chain 'p' and resid 24 through 34 Processing helix chain 'p' and resid 34 through 42 Processing helix chain 'p' and resid 43 through 56 Proline residue: p 53 - end of helix Processing helix chain 'p' and resid 64 through 75 removed outlier: 4.361A pdb=" N ALA p 68 " --> pdb=" O GLU p 64 " (cutoff:3.500A) Processing helix chain 'p' and resid 82 through 98 removed outlier: 4.689A pdb=" N CYS p 88 " --> pdb=" O GLU p 84 " (cutoff:3.500A) Proline residue: p 91 - end of helix Processing helix chain 'p' and resid 101 through 119 Processing helix chain 'p' and resid 120 through 137 Proline residue: p 130 - end of helix Processing helix chain 'p' and resid 140 through 155 removed outlier: 3.746A pdb=" N ARG p 144 " --> pdb=" O TRP p 140 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY p 149 " --> pdb=" O THR p 145 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU p 150 " --> pdb=" O SER p 146 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE p 151 " --> pdb=" O ALA p 147 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER p 152 " --> pdb=" O CYS p 148 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL p 153 " --> pdb=" O GLY p 149 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS p 154 " --> pdb=" O LEU p 150 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR p 155 " --> pdb=" O PHE p 151 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 175 removed outlier: 3.732A pdb=" N SER p 175 " --> pdb=" O ARG p 171 " (cutoff:3.500A) Processing helix chain 'p' and resid 178 through 188 removed outlier: 3.666A pdb=" N ARG p 182 " --> pdb=" O THR p 178 " (cutoff:3.500A) Processing helix chain 'p' and resid 188 through 196 Processing helix chain 'p' and resid 197 through 214 Proline residue: p 207 - end of helix Processing helix chain 'p' and resid 217 through 231 Processing helix chain 'p' and resid 236 through 253 Proline residue: p 246 - end of helix Processing helix chain 'p' and resid 256 through 266 Processing helix chain 'p' and resid 266 through 274 removed outlier: 3.657A pdb=" N LEU p 270 " --> pdb=" O LYS p 266 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL p 274 " --> pdb=" O LEU p 270 " (cutoff:3.500A) Processing helix chain 'p' and resid 275 through 292 Proline residue: p 285 - end of helix Processing helix chain 'p' and resid 295 through 312 removed outlier: 3.596A pdb=" N ARG p 299 " --> pdb=" O GLU p 295 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS p 307 " --> pdb=" O SER p 303 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU p 308 " --> pdb=" O HIS p 304 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN p 312 " --> pdb=" O GLU p 308 " (cutoff:3.500A) Processing helix chain 'p' and resid 314 through 335 removed outlier: 4.700A pdb=" N GLU p 319 " --> pdb=" O ALA p 315 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASN p 320 " --> pdb=" O ASP p 316 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU p 327 " --> pdb=" O MET p 323 " (cutoff:3.500A) Proline residue: p 328 - end of helix removed outlier: 3.965A pdb=" N SER p 335 " --> pdb=" O LYS p 331 " (cutoff:3.500A) Processing helix chain 'p' and resid 338 through 349 removed outlier: 3.814A pdb=" N LYS p 342 " --> pdb=" O ASN p 338 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL p 348 " --> pdb=" O ALA p 344 " (cutoff:3.500A) Processing helix chain 'p' and resid 352 through 357 Processing helix chain 'p' and resid 357 through 364 Processing helix chain 'p' and resid 364 through 374 removed outlier: 4.081A pdb=" N LEU p 368 " --> pdb=" O HIS p 364 " (cutoff:3.500A) Processing helix chain 'p' and resid 377 through 386 removed outlier: 3.527A pdb=" N SER p 386 " --> pdb=" O LEU p 382 " (cutoff:3.500A) Processing helix chain 'p' and resid 387 through 396 removed outlier: 4.125A pdb=" N VAL p 391 " --> pdb=" O ASN p 387 " (cutoff:3.500A) Processing helix chain 'p' and resid 396 through 404 Processing helix chain 'p' and resid 404 through 413 removed outlier: 3.692A pdb=" N GLU p 413 " --> pdb=" O VAL p 409 " (cutoff:3.500A) Processing helix chain 'p' and resid 416 through 425 Processing helix chain 'p' and resid 426 through 433 Processing helix chain 'p' and resid 435 through 443 Processing helix chain 'p' and resid 443 through 452 removed outlier: 3.836A pdb=" N LEU p 451 " --> pdb=" O CYS p 447 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL p 452 " --> pdb=" O MET p 448 " (cutoff:3.500A) Processing helix chain 'p' and resid 455 through 473 Processing helix chain 'p' and resid 475 through 491 removed outlier: 4.522A pdb=" N ILE p 483 " --> pdb=" O HIS p 479 " (cutoff:3.500A) Proline residue: p 484 - end of helix removed outlier: 3.654A pdb=" N GLY p 491 " --> pdb=" O LEU p 487 " (cutoff:3.500A) Processing helix chain 'p' and resid 494 through 511 removed outlier: 3.767A pdb=" N ARG p 498 " --> pdb=" O ASN p 494 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU p 510 " --> pdb=" O ASN p 506 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL p 511 " --> pdb=" O VAL p 507 " (cutoff:3.500A) Processing helix chain 'p' and resid 513 through 528 Proline residue: p 523 - end of helix removed outlier: 3.615A pdb=" N MET p 528 " --> pdb=" O THR p 524 " (cutoff:3.500A) Processing helix chain 'p' and resid 529 through 531 No H-bonds generated for 'chain 'p' and resid 529 through 531' Processing helix chain 'p' and resid 533 through 547 Processing helix chain 'p' and resid 552 through 569 Proline residue: p 562 - end of helix removed outlier: 3.650A pdb=" N GLN p 569 " --> pdb=" O GLU p 565 " (cutoff:3.500A) Processing helix chain 'p' and resid 572 through 587 Processing helix chain 'q' and resid 7 through 19 removed outlier: 3.635A pdb=" N GLU q 19 " --> pdb=" O GLU q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 40 Processing helix chain 'q' and resid 61 through 73 Processing helix chain 'q' and resid 92 through 107 Processing helix chain 'q' and resid 120 through 128 removed outlier: 3.530A pdb=" N GLY q 128 " --> pdb=" O THR q 124 " (cutoff:3.500A) Processing helix chain 'q' and resid 128 through 138 Processing helix chain 'q' and resid 140 through 151 removed outlier: 3.860A pdb=" N ASP q 151 " --> pdb=" O THR q 147 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 182 Processing helix chain 'q' and resid 193 through 201 Processing helix chain 'q' and resid 221 through 233 Processing helix chain 'r' and resid 48 through 58 removed outlier: 3.755A pdb=" N MET r 58 " --> pdb=" O LEU r 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 656 through 667 Processing helix chain 'm' and resid 672 through 677 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 removed outlier: 4.234A pdb=" N PHE B 21 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE B 68 " --> pdb=" O PHE B 21 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE B 67 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 71 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 91 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 44 removed outlier: 9.917A pdb=" N SER B 49 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N LEU B 84 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN B 51 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR B 85 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR B 74 " --> pdb=" O TYR B 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 1159 through 1163 Processing sheet with id=AA4, first strand: chain 'd' and resid 267 through 269 Processing sheet with id=AA5, first strand: chain 'd' and resid 711 through 712 removed outlier: 3.665A pdb=" N HIS d 818 " --> pdb=" O SER d 712 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 821 through 824 removed outlier: 3.527A pdb=" N SER d 821 " --> pdb=" O GLU d 852 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR d 823 " --> pdb=" O THR d 850 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 835 through 838 removed outlier: 5.946A pdb=" N LEU d 835 " --> pdb=" O MET d 957 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS d 959 " --> pdb=" O LEU d 835 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE d 837 " --> pdb=" O LYS d 959 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 835 through 838 removed outlier: 5.946A pdb=" N LEU d 835 " --> pdb=" O MET d 957 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS d 959 " --> pdb=" O LEU d 835 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE d 837 " --> pdb=" O LYS d 959 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 960 through 963 Processing sheet with id=AB1, first strand: chain 'f' and resid 62 through 64 removed outlier: 6.564A pdb=" N ILE f 3 " --> pdb=" O ILE f 124 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE f 126 " --> pdb=" O ILE f 3 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU f 5 " --> pdb=" O ILE f 126 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE f 128 " --> pdb=" O LEU f 5 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU f 7 " --> pdb=" O ILE f 128 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASP f 130 " --> pdb=" O LEU f 7 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA f 123 " --> pdb=" O ARG f 167 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N PHE f 169 " --> pdb=" O ALA f 123 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE f 125 " --> pdb=" O PHE f 169 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU f 171 " --> pdb=" O ILE f 125 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR f 127 " --> pdb=" O LEU f 171 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU f 173 " --> pdb=" O THR f 127 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR f 129 " --> pdb=" O LEU f 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 230 through 238 removed outlier: 3.952A pdb=" N GLU f 328 " --> pdb=" O TYR f 269 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP f 325 " --> pdb=" O VAL f 381 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL f 377 " --> pdb=" O LEU f 329 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY f 366 " --> pdb=" O VAL f 350 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS f 347 " --> pdb=" O THR f 312 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR f 312 " --> pdb=" O CYS f 347 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN f 349 " --> pdb=" O SER f 310 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS f 311 " --> pdb=" O ALA f 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'g' and resid 807 through 808 removed outlier: 3.548A pdb=" N GLY g 833 " --> pdb=" O PHE g 888 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE g 888 " --> pdb=" O GLY g 833 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 820 through 822 removed outlier: 3.510A pdb=" N LEU g 931 " --> pdb=" O VAL g 821 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL g 854 " --> pdb=" O MET g 877 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET g 877 " --> pdb=" O VAL g 854 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'g' and resid 820 through 822 removed outlier: 3.510A pdb=" N LEU g 931 " --> pdb=" O VAL g 821 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'i' and resid 194 through 196 removed outlier: 6.249A pdb=" N ILE i 99 " --> pdb=" O TYR i 124 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL i 98 " --> pdb=" O THR i 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'i' and resid 68 through 71 Processing sheet with id=AB8, first strand: chain 'i' and resid 83 through 84 Processing sheet with id=AB9, first strand: chain 'i' and resid 203 through 205 removed outlier: 3.547A pdb=" N VAL i 260 " --> pdb=" O LYS i 233 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N TYR i 499 " --> pdb=" O VAL i 469 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N CYS i 471 " --> pdb=" O TYR i 499 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'i' and resid 374 through 376 removed outlier: 5.680A pdb=" N LEU i 326 " --> pdb=" O LYS i 374 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR i 376 " --> pdb=" O LEU i 326 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE i 328 " --> pdb=" O TYR i 376 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR i 327 " --> pdb=" O PHE i 394 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL i 295 " --> pdb=" O VAL i 393 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR i 395 " --> pdb=" O VAL i 295 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL i 297 " --> pdb=" O THR i 395 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU i 296 " --> pdb=" O ILE i 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'i' and resid 513 through 518 removed outlier: 11.917A pdb=" N HIS i 551 " --> pdb=" O TYR i 513 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LYS i 515 " --> pdb=" O HIS i 551 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LEU i 553 " --> pdb=" O LYS i 515 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU i 517 " --> pdb=" O LEU i 553 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN i 554 " --> pdb=" O VAL i 543 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA i 538 " --> pdb=" O LEU k 483 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG k 491 " --> pdb=" O ILE k 484 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY k 455 " --> pdb=" O LEU k 492 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL k 454 " --> pdb=" O ILE i 516 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU i 514 " --> pdb=" O ILE k 456 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'i' and resid 616 through 619 removed outlier: 3.616A pdb=" N VAL i 617 " --> pdb=" O ILE i 626 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE i 626 " --> pdb=" O VAL i 617 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN i 627 " --> pdb=" O HIS i 634 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS i 634 " --> pdb=" O GLN i 627 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU i 629 " --> pdb=" O SER i 632 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'j' and resid 346 through 348 removed outlier: 3.589A pdb=" N LEU j 553 " --> pdb=" O VAL j 346 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU j 348 " --> pdb=" O LYS j 551 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'k' and resid 61 through 64 removed outlier: 7.323A pdb=" N ASN k 28 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS k 63 " --> pdb=" O ASN k 28 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG k 5 " --> pdb=" O SER k 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'k' and resid 91 through 93 removed outlier: 6.067A pdb=" N MET k 92 " --> pdb=" O VAL k 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'k' and resid 148 through 154 removed outlier: 3.690A pdb=" N LYS k 167 " --> pdb=" O GLU k 149 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER k 172 " --> pdb=" O LEU k 199 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE k 201 " --> pdb=" O SER k 172 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL k 174 " --> pdb=" O ILE k 201 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N GLN k 203 " --> pdb=" O VAL k 174 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU k 200 " --> pdb=" O LEU k 411 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL k 413 " --> pdb=" O LEU k 200 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N THR k 202 " --> pdb=" O VAL k 413 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'k' and resid 235 through 238 removed outlier: 3.964A pdb=" N VAL k 321 " --> pdb=" O VAL k 235 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA k 323 " --> pdb=" O ILE k 237 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'k' and resid 512 through 516 removed outlier: 3.761A pdb=" N VAL k 515 " --> pdb=" O LEU k 572 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU k 572 " --> pdb=" O VAL k 515 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'k' and resid 551 through 553 removed outlier: 3.626A pdb=" N VAL k 551 " --> pdb=" O LEU k 558 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU k 558 " --> pdb=" O VAL k 551 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL k 553 " --> pdb=" O VAL k 556 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'q' and resid 45 through 48 removed outlier: 6.480A pdb=" N VAL q 237 " --> pdb=" O VAL q 257 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE q 259 " --> pdb=" O VAL q 237 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG q 239 " --> pdb=" O ILE q 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'q' and resid 111 through 114 removed outlier: 6.482A pdb=" N TYR q 80 " --> pdb=" O THR q 112 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU q 114 " --> pdb=" O TYR q 80 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE q 82 " --> pdb=" O LEU q 114 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'q' and resid 202 through 203 removed outlier: 6.873A pdb=" N ASP q 202 " --> pdb=" O PHE q 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 4838 hydrogen bonds defined for protein. 14172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 31.53 Time building geometry restraints manager: 26.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 24554 1.34 - 1.46: 14568 1.46 - 1.58: 35696 1.58 - 1.70: 0 1.70 - 1.82: 609 Bond restraints: 75427 Sorted by residual: bond pdb=" C LEU k 77 " pdb=" N PRO k 78 " ideal model delta sigma weight residual 1.335 1.389 -0.054 1.30e-02 5.92e+03 1.74e+01 bond pdb=" C PRO b 871 " pdb=" N PRO b 872 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" C GLU c 100 " pdb=" N PRO c 101 " ideal model delta sigma weight residual 1.335 1.371 -0.035 1.30e-02 5.92e+03 7.38e+00 bond pdb=" C VAL p 284 " pdb=" N PRO p 285 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.61e+00 bond pdb=" C HIS i 246 " pdb=" N PRO i 247 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.51e+00 ... (remaining 75422 not shown) Histogram of bond angle deviations from ideal: 95.37 - 103.29: 671 103.29 - 111.22: 30894 111.22 - 119.14: 31398 119.14 - 127.06: 38829 127.06 - 134.98: 930 Bond angle restraints: 102722 Sorted by residual: angle pdb=" C VAL a1629 " pdb=" N VAL a1630 " pdb=" CA VAL a1630 " ideal model delta sigma weight residual 121.97 130.92 -8.95 1.80e+00 3.09e-01 2.47e+01 angle pdb=" N PRO e 568 " pdb=" CA PRO e 568 " pdb=" C PRO e 568 " ideal model delta sigma weight residual 110.70 115.66 -4.96 1.22e+00 6.72e-01 1.65e+01 angle pdb=" C HIS g 884 " pdb=" N ASN g 885 " pdb=" CA ASN g 885 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C ASN m 680 " pdb=" N ASN m 681 " pdb=" CA ASN m 681 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C GLN h 744 " pdb=" N ARG h 745 " pdb=" CA ARG h 745 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 ... (remaining 102717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 42329 17.93 - 35.85: 2563 35.85 - 53.78: 583 53.78 - 71.71: 120 71.71 - 89.64: 64 Dihedral angle restraints: 45659 sinusoidal: 16118 harmonic: 29541 Sorted by residual: dihedral pdb=" CA PHE h 407 " pdb=" C PHE h 407 " pdb=" N LEU h 408 " pdb=" CA LEU h 408 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ILE p 205 " pdb=" C ILE p 205 " pdb=" N ILE p 206 " pdb=" CA ILE p 206 " ideal model delta harmonic sigma weight residual 180.00 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA PRO q 263 " pdb=" C PRO q 263 " pdb=" N ASN q 264 " pdb=" CA ASN q 264 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 45656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 10968 0.081 - 0.161: 1256 0.161 - 0.242: 80 0.242 - 0.322: 4 0.322 - 0.403: 2 Chirality restraints: 12310 Sorted by residual: chirality pdb=" CB VAL e 930 " pdb=" CA VAL e 930 " pdb=" CG1 VAL e 930 " pdb=" CG2 VAL e 930 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB ILE g 133 " pdb=" CA ILE g 133 " pdb=" CG1 ILE g 133 " pdb=" CG2 ILE g 133 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE g 59 " pdb=" CA ILE g 59 " pdb=" CG1 ILE g 59 " pdb=" CG2 ILE g 59 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 12307 not shown) Planarity restraints: 13256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL e 667 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.52e+00 pdb=" C VAL e 667 " 0.053 2.00e-02 2.50e+03 pdb=" O VAL e 667 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA e 668 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE b 787 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO b 788 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO b 788 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO b 788 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 230 " -0.013 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C ILE b 230 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE b 230 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS b 231 " -0.015 2.00e-02 2.50e+03 ... (remaining 13253 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2592 2.73 - 3.27: 79233 3.27 - 3.81: 124677 3.81 - 4.36: 142306 4.36 - 4.90: 242481 Nonbonded interactions: 591289 Sorted by model distance: nonbonded pdb=" O ILE i 113 " pdb=" OG1 THR i 117 " model vdw 2.184 2.440 nonbonded pdb=" OD1 ASP h 841 " pdb=" OH TYR h 856 " model vdw 2.197 2.440 nonbonded pdb=" O LEU e 677 " pdb=" OG1 THR e 680 " model vdw 2.198 2.440 nonbonded pdb=" O GLU b 528 " pdb=" OG1 THR b 532 " model vdw 2.198 2.440 nonbonded pdb=" O LEU a1070 " pdb=" OG1 THR a1074 " model vdw 2.204 2.440 ... (remaining 591284 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: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 21.470 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 166.100 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.004 0.069 75427 Z= 0.297 Angle : 0.848 12.654 102722 Z= 0.434 Chirality : 0.050 0.403 12310 Planarity : 0.005 0.065 13256 Dihedral : 13.319 89.637 26349 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 0.25 % Allowed : 8.04 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 9922 helix: 2.11 (0.07), residues: 6364 sheet: -0.33 (0.24), residues: 473 loop : -0.71 (0.12), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP k 576 HIS 0.014 0.001 HIS b 534 PHE 0.022 0.002 PHE g 108 TYR 0.026 0.002 TYR h 271 ARG 0.009 0.001 ARG b 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 991 time to evaluate : 6.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 2127 TYR cc_start: 0.8296 (t80) cc_final: 0.7742 (t80) REVERT: a 2157 VAL cc_start: 0.7651 (p) cc_final: 0.7152 (t) REVERT: a 2171 MET cc_start: 0.7643 (pmm) cc_final: 0.7222 (ptp) REVERT: b 435 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7760 (mmm) REVERT: b 479 MET cc_start: 0.8033 (ptm) cc_final: 0.7601 (tmm) REVERT: b 645 ILE cc_start: 0.8506 (tp) cc_final: 0.8249 (mm) REVERT: b 782 SER cc_start: 0.8806 (t) cc_final: 0.8537 (m) REVERT: b 1128 ILE cc_start: 0.8714 (tt) cc_final: 0.8387 (tp) REVERT: b 1182 ASP cc_start: 0.7389 (m-30) cc_final: 0.6816 (m-30) REVERT: c 90 CYS cc_start: 0.5956 (m) cc_final: 0.5639 (m) REVERT: d 96 LEU cc_start: 0.9803 (mm) cc_final: 0.9585 (mt) REVERT: d 220 LEU cc_start: 0.9354 (mt) cc_final: 0.8915 (mt) REVERT: d 688 LYS cc_start: 0.8126 (ptmm) cc_final: 0.7823 (tttm) REVERT: d 701 MET cc_start: 0.8928 (mmm) cc_final: 0.8703 (mmm) REVERT: e 577 ASN cc_start: 0.8601 (m-40) cc_final: 0.8388 (m110) REVERT: f 91 SER cc_start: 0.8744 (m) cc_final: 0.8166 (t) REVERT: f 98 LEU cc_start: 0.8629 (tp) cc_final: 0.8368 (tp) REVERT: f 554 ASP cc_start: 0.8062 (m-30) cc_final: 0.7464 (t0) REVERT: g 89 GLN cc_start: 0.7176 (mt0) cc_final: 0.6689 (mm-40) REVERT: g 204 MET cc_start: 0.8839 (mmp) cc_final: 0.8575 (mmt) REVERT: g 275 ASP cc_start: 0.7159 (m-30) cc_final: 0.6883 (m-30) REVERT: g 304 TYR cc_start: 0.7192 (m-80) cc_final: 0.6771 (m-80) REVERT: g 450 CYS cc_start: 0.8980 (m) cc_final: 0.8551 (m) REVERT: g 463 LEU cc_start: 0.7657 (pt) cc_final: 0.6915 (pp) REVERT: g 474 LEU cc_start: 0.9023 (tp) cc_final: 0.8762 (tp) REVERT: g 843 LEU cc_start: 0.9053 (tp) cc_final: 0.8831 (tp) REVERT: g 892 PHE cc_start: 0.8958 (m-80) cc_final: 0.8743 (m-80) REVERT: h 458 MET cc_start: 0.8875 (ptm) cc_final: 0.8669 (ptt) REVERT: h 774 LEU cc_start: 0.9011 (mt) cc_final: 0.8804 (tp) REVERT: i 25 MET cc_start: 0.8718 (tmm) cc_final: 0.8487 (tmm) REVERT: k 30 MET cc_start: 0.6352 (tpt) cc_final: 0.6139 (tpp) REVERT: k 130 MET cc_start: 0.8641 (ttm) cc_final: 0.8097 (tpt) REVERT: k 204 SER cc_start: 0.7914 (OUTLIER) cc_final: 0.7687 (p) REVERT: k 289 LYS cc_start: 0.5886 (tttt) cc_final: 0.5444 (pptt) REVERT: k 420 MET cc_start: 0.8153 (ptp) cc_final: 0.7090 (ptp) REVERT: p 304 HIS cc_start: 0.8044 (m170) cc_final: 0.7801 (m-70) REVERT: q 66 MET cc_start: 0.8214 (mmm) cc_final: 0.7995 (mmm) REVERT: q 145 TYR cc_start: 0.7431 (m-10) cc_final: 0.7194 (m-80) REVERT: r 49 ASP cc_start: 0.8580 (p0) cc_final: 0.8324 (p0) outliers start: 18 outliers final: 4 residues processed: 1004 average time/residue: 0.6746 time to fit residues: 1162.0482 Evaluate side-chains 572 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 566 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1630 VAL Chi-restraints excluded: chain b residue 435 MET Chi-restraints excluded: chain e residue 181 MET Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain k residue 204 SER Chi-restraints excluded: chain k residue 302 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 845 optimal weight: 8.9990 chunk 758 optimal weight: 8.9990 chunk 420 optimal weight: 0.0060 chunk 259 optimal weight: 9.9990 chunk 511 optimal weight: 0.5980 chunk 405 optimal weight: 0.9990 chunk 784 optimal weight: 50.0000 chunk 303 optimal weight: 6.9990 chunk 477 optimal weight: 6.9990 chunk 583 optimal weight: 5.9990 chunk 909 optimal weight: 0.0870 overall best weight: 1.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2176 GLN ** b 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 203 HIS b 879 HIS b1048 GLN ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 HIS d 699 GLN e 499 GLN f 70 HIS f 462 GLN ** g 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 885 ASN h 445 ASN ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 314 GLN k 287 ASN p 30 ASN ** p 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 75427 Z= 0.258 Angle : 0.613 11.572 102722 Z= 0.305 Chirality : 0.041 0.234 12310 Planarity : 0.004 0.063 13256 Dihedral : 4.107 55.698 10650 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 1.45 % Allowed : 11.67 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.09), residues: 9922 helix: 2.00 (0.07), residues: 6457 sheet: -0.41 (0.24), residues: 482 loop : -0.63 (0.12), residues: 2983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 337 HIS 0.016 0.001 HIS p 520 PHE 0.018 0.002 PHE i 339 TYR 0.026 0.001 TYR b 486 ARG 0.009 0.001 ARG g 666 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 588 time to evaluate : 6.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 2171 MET cc_start: 0.8056 (pmm) cc_final: 0.7728 (ptp) REVERT: b 188 LEU cc_start: 0.7712 (mm) cc_final: 0.7379 (mm) REVERT: b 211 LEU cc_start: 0.8791 (mt) cc_final: 0.8541 (mt) REVERT: b 435 MET cc_start: 0.8344 (mmm) cc_final: 0.8027 (mmt) REVERT: b 479 MET cc_start: 0.8095 (ptm) cc_final: 0.7777 (tmm) REVERT: b 645 ILE cc_start: 0.8411 (tp) cc_final: 0.8097 (mm) REVERT: b 743 MET cc_start: 0.8955 (tpp) cc_final: 0.8593 (tpp) REVERT: b 782 SER cc_start: 0.8905 (t) cc_final: 0.8515 (m) REVERT: b 1035 MET cc_start: 0.8756 (mmm) cc_final: 0.8538 (tpp) REVERT: b 1128 ILE cc_start: 0.8709 (tt) cc_final: 0.8355 (tp) REVERT: d 96 LEU cc_start: 0.9810 (mm) cc_final: 0.9606 (mt) REVERT: d 111 MET cc_start: 0.9436 (ptp) cc_final: 0.8994 (ppp) REVERT: d 219 MET cc_start: 0.8920 (mmm) cc_final: 0.8630 (mmm) REVERT: d 687 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.7924 (pp) REVERT: d 701 MET cc_start: 0.8950 (mmm) cc_final: 0.8725 (mmm) REVERT: d 725 MET cc_start: 0.8535 (tpp) cc_final: 0.8130 (mpp) REVERT: d 784 MET cc_start: 0.9194 (tpp) cc_final: 0.8718 (tpp) REVERT: d 802 MET cc_start: 0.8564 (tpp) cc_final: 0.8303 (tpt) REVERT: e 181 MET cc_start: 0.3437 (OUTLIER) cc_final: 0.2399 (mmt) REVERT: e 746 TRP cc_start: 0.4900 (p-90) cc_final: 0.4647 (p-90) REVERT: f 51 MET cc_start: 0.7110 (mmt) cc_final: 0.6652 (mmt) REVERT: f 91 SER cc_start: 0.8768 (m) cc_final: 0.8199 (t) REVERT: f 554 ASP cc_start: 0.8256 (m-30) cc_final: 0.7657 (t0) REVERT: g 275 ASP cc_start: 0.7330 (m-30) cc_final: 0.7084 (m-30) REVERT: g 450 CYS cc_start: 0.9022 (m) cc_final: 0.8609 (m) REVERT: g 463 LEU cc_start: 0.7806 (pt) cc_final: 0.7149 (pp) REVERT: g 473 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: g 474 LEU cc_start: 0.9201 (tp) cc_final: 0.8963 (tp) REVERT: g 541 MET cc_start: 0.7833 (tpp) cc_final: 0.7370 (tpp) REVERT: g 700 LEU cc_start: 0.8753 (mt) cc_final: 0.8546 (mt) REVERT: i 25 MET cc_start: 0.8784 (tmm) cc_final: 0.8415 (tmm) REVERT: k 30 MET cc_start: 0.7003 (tpt) cc_final: 0.6753 (tpp) REVERT: k 35 MET cc_start: 0.8218 (tmm) cc_final: 0.7889 (tmm) REVERT: k 130 MET cc_start: 0.8613 (ttm) cc_final: 0.8100 (tpt) REVERT: k 319 MET cc_start: 0.2697 (tpt) cc_final: 0.2493 (tpt) REVERT: k 420 MET cc_start: 0.7959 (ptp) cc_final: 0.7080 (ptp) REVERT: q 49 ARG cc_start: 0.7665 (mmm-85) cc_final: 0.7437 (mmm160) REVERT: q 186 LEU cc_start: 0.8924 (mt) cc_final: 0.8707 (mt) REVERT: r 39 GLU cc_start: 0.7849 (mp0) cc_final: 0.6642 (pm20) outliers start: 106 outliers final: 53 residues processed: 669 average time/residue: 0.7051 time to fit residues: 841.8907 Evaluate side-chains 562 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 506 time to evaluate : 6.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1704 VAL Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 2080 ILE Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 398 ILE Chi-restraints excluded: chain b residue 538 VAL Chi-restraints excluded: chain b residue 726 ASP Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1108 VAL Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 241 LEU Chi-restraints excluded: chain d residue 455 VAL Chi-restraints excluded: chain d residue 467 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 866 LEU Chi-restraints excluded: chain e residue 181 MET Chi-restraints excluded: chain e residue 438 LEU Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain f residue 105 VAL Chi-restraints excluded: chain f residue 219 CYS Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 529 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 473 GLU Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 885 ASN Chi-restraints excluded: chain g residue 905 THR Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 920 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 157 SER Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 489 ASN Chi-restraints excluded: chain h residue 530 ILE Chi-restraints excluded: chain h residue 741 LEU Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain i residue 519 MET Chi-restraints excluded: chain k residue 204 SER Chi-restraints excluded: chain p residue 30 ASN Chi-restraints excluded: chain p residue 117 HIS Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain r residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 505 optimal weight: 0.2980 chunk 282 optimal weight: 5.9990 chunk 756 optimal weight: 9.9990 chunk 618 optimal weight: 1.9990 chunk 250 optimal weight: 50.0000 chunk 910 optimal weight: 5.9990 chunk 983 optimal weight: 0.9990 chunk 811 optimal weight: 20.0000 chunk 903 optimal weight: 50.0000 chunk 310 optimal weight: 5.9990 chunk 730 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 GLN g 76 ASN g 140 HIS ** g 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 826 GLN h 307 GLN h 445 ASN ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 252 GLN p 304 HIS ** p 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 360 ASN ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 75427 Z= 0.371 Angle : 0.637 10.077 102722 Z= 0.318 Chirality : 0.042 0.318 12310 Planarity : 0.004 0.053 13256 Dihedral : 4.094 40.178 10644 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 2.11 % Allowed : 13.08 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.09), residues: 9922 helix: 1.85 (0.07), residues: 6429 sheet: -0.37 (0.25), residues: 450 loop : -0.73 (0.12), residues: 3043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP k 256 HIS 0.024 0.001 HIS p 304 PHE 0.032 0.002 PHE h 54 TYR 0.031 0.002 TYR b 486 ARG 0.016 0.001 ARG b 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 530 time to evaluate : 6.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 435 MET cc_start: 0.8442 (mmm) cc_final: 0.8155 (mmt) REVERT: b 479 MET cc_start: 0.8145 (ptm) cc_final: 0.7795 (tmm) REVERT: b 645 ILE cc_start: 0.8469 (tp) cc_final: 0.8150 (mm) REVERT: b 1104 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8255 (mp) REVERT: b 1128 ILE cc_start: 0.8721 (tt) cc_final: 0.8363 (tp) REVERT: c 131 MET cc_start: 0.5799 (ppp) cc_final: 0.5472 (ppp) REVERT: d 111 MET cc_start: 0.9462 (ptp) cc_final: 0.9055 (ppp) REVERT: d 219 MET cc_start: 0.9072 (mmm) cc_final: 0.8765 (mmm) REVERT: d 725 MET cc_start: 0.8623 (tpp) cc_final: 0.8209 (mpp) REVERT: e 152 MET cc_start: 0.8417 (mmp) cc_final: 0.8038 (mmt) REVERT: f 91 SER cc_start: 0.8828 (m) cc_final: 0.8257 (t) REVERT: f 434 MET cc_start: 0.5796 (mmm) cc_final: 0.5055 (mmm) REVERT: f 554 ASP cc_start: 0.8323 (m-30) cc_final: 0.7807 (t0) REVERT: g 102 GLU cc_start: 0.7887 (tp30) cc_final: 0.7398 (tp30) REVERT: g 275 ASP cc_start: 0.7634 (m-30) cc_final: 0.7177 (m-30) REVERT: g 450 CYS cc_start: 0.9060 (m) cc_final: 0.8625 (m) REVERT: g 541 MET cc_start: 0.7924 (tpp) cc_final: 0.7538 (tpp) REVERT: h 141 MET cc_start: 0.1499 (ptt) cc_final: 0.1071 (mtt) REVERT: i 25 MET cc_start: 0.8750 (tmm) cc_final: 0.8186 (tmm) REVERT: i 277 MET cc_start: 0.8991 (mmp) cc_final: 0.7981 (mmt) REVERT: k 130 MET cc_start: 0.8603 (ttm) cc_final: 0.8070 (tpt) REVERT: k 319 MET cc_start: 0.2855 (tpt) cc_final: 0.2374 (tpt) REVERT: k 420 MET cc_start: 0.7968 (ptp) cc_final: 0.7137 (ptp) REVERT: q 122 GLN cc_start: 0.7715 (mp10) cc_final: 0.7453 (mp10) REVERT: q 186 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8679 (mt) REVERT: r 38 GLU cc_start: 0.7524 (pm20) cc_final: 0.6522 (pm20) REVERT: r 39 GLU cc_start: 0.7561 (mp0) cc_final: 0.6503 (pm20) outliers start: 154 outliers final: 85 residues processed: 652 average time/residue: 0.6314 time to fit residues: 736.2543 Evaluate side-chains 568 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 481 time to evaluate : 6.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1511 ARG Chi-restraints excluded: chain a residue 1704 VAL Chi-restraints excluded: chain a residue 2063 LEU Chi-restraints excluded: chain a residue 2080 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 345 LEU Chi-restraints excluded: chain b residue 396 MET Chi-restraints excluded: chain b residue 398 ILE Chi-restraints excluded: chain b residue 523 GLN Chi-restraints excluded: chain b residue 726 ASP Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 896 LEU Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1104 LEU Chi-restraints excluded: chain b residue 1108 VAL Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 241 LEU Chi-restraints excluded: chain d residue 467 LEU Chi-restraints excluded: chain d residue 493 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 691 ASP Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 823 THR Chi-restraints excluded: chain d residue 866 LEU Chi-restraints excluded: chain e residue 438 LEU Chi-restraints excluded: chain e residue 477 LEU Chi-restraints excluded: chain e residue 498 TRP Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain f residue 219 CYS Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 529 VAL Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 460 LEU Chi-restraints excluded: chain g residue 473 GLU Chi-restraints excluded: chain g residue 601 ILE Chi-restraints excluded: chain g residue 692 SER Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 717 ILE Chi-restraints excluded: chain g residue 769 VAL Chi-restraints excluded: chain g residue 890 THR Chi-restraints excluded: chain g residue 905 THR Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 260 TYR Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 457 PHE Chi-restraints excluded: chain h residue 458 MET Chi-restraints excluded: chain h residue 489 ASN Chi-restraints excluded: chain h residue 717 LEU Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 778 VAL Chi-restraints excluded: chain h residue 895 THR Chi-restraints excluded: chain h residue 906 GLU Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain i residue 309 LEU Chi-restraints excluded: chain i residue 545 HIS Chi-restraints excluded: chain k residue 204 SER Chi-restraints excluded: chain k residue 289 LYS Chi-restraints excluded: chain k residue 302 PHE Chi-restraints excluded: chain k residue 348 VAL Chi-restraints excluded: chain k residue 448 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 103 VAL Chi-restraints excluded: chain p residue 117 HIS Chi-restraints excluded: chain p residue 353 SER Chi-restraints excluded: chain p residue 430 LEU Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 186 LEU Chi-restraints excluded: chain q residue 202 ASP Chi-restraints excluded: chain q residue 278 LEU Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 52 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 899 optimal weight: 30.0000 chunk 684 optimal weight: 9.9990 chunk 472 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 434 optimal weight: 0.6980 chunk 611 optimal weight: 2.9990 chunk 913 optimal weight: 7.9990 chunk 967 optimal weight: 3.9990 chunk 477 optimal weight: 4.9990 chunk 866 optimal weight: 50.0000 chunk 260 optimal weight: 0.0370 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 580 GLN b 802 ASN b1198 ASN ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 GLN f 110 ASN ** f 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 203 HIS g 205 HIS g 439 HIS g 573 GLN ** g 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 885 ASN h 445 ASN ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 656 GLN p 30 ASN p 288 GLN ** p 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 535 ASN ** q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 669 HIS m 670 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 75427 Z= 0.351 Angle : 0.619 12.089 102722 Z= 0.309 Chirality : 0.041 0.344 12310 Planarity : 0.004 0.053 13256 Dihedral : 4.091 38.808 10641 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.40 % Allowed : 14.07 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.09), residues: 9922 helix: 1.80 (0.07), residues: 6440 sheet: -0.39 (0.25), residues: 464 loop : -0.78 (0.12), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 902 HIS 0.011 0.001 HIS e 888 PHE 0.044 0.002 PHE h 54 TYR 0.027 0.002 TYR b 486 ARG 0.008 0.000 ARG q 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 508 time to evaluate : 6.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 2159 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8728 (mm) REVERT: a 2171 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7522 (ptp) REVERT: b 435 MET cc_start: 0.8470 (mmm) cc_final: 0.8078 (mmt) REVERT: b 479 MET cc_start: 0.8250 (ptm) cc_final: 0.7793 (tmm) REVERT: b 1104 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8255 (mp) REVERT: c 121 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5798 (mp) REVERT: c 419 MET cc_start: 0.2412 (mmp) cc_final: 0.2206 (mmp) REVERT: d 111 MET cc_start: 0.9477 (ptp) cc_final: 0.9044 (ppp) REVERT: d 219 MET cc_start: 0.9069 (mmm) cc_final: 0.8843 (mmm) REVERT: d 400 MET cc_start: 0.8490 (mpp) cc_final: 0.8166 (mpp) REVERT: d 725 MET cc_start: 0.8602 (tpp) cc_final: 0.8164 (mpp) REVERT: d 784 MET cc_start: 0.9359 (tpp) cc_final: 0.8743 (tpp) REVERT: d 874 MET cc_start: 0.8198 (ttt) cc_final: 0.7900 (ttt) REVERT: e 181 MET cc_start: 0.4151 (mpt) cc_final: 0.3464 (mpt) REVERT: f 91 SER cc_start: 0.8837 (m) cc_final: 0.8209 (t) REVERT: f 434 MET cc_start: 0.5549 (mmm) cc_final: 0.4879 (mmm) REVERT: f 554 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7688 (t0) REVERT: g 102 GLU cc_start: 0.8052 (tp30) cc_final: 0.7541 (tp30) REVERT: g 275 ASP cc_start: 0.7744 (m-30) cc_final: 0.7274 (m-30) REVERT: g 450 CYS cc_start: 0.9025 (m) cc_final: 0.8565 (m) REVERT: g 541 MET cc_start: 0.7903 (tpp) cc_final: 0.7579 (tpp) REVERT: g 845 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8768 (mmt-90) REVERT: h 141 MET cc_start: 0.1814 (ptt) cc_final: 0.1538 (mtm) REVERT: i 25 MET cc_start: 0.8731 (tmm) cc_final: 0.8085 (tmm) REVERT: i 444 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8222 (mp) REVERT: k 130 MET cc_start: 0.8582 (ttm) cc_final: 0.8088 (tpt) REVERT: k 181 MET cc_start: 0.8011 (mmm) cc_final: 0.7656 (mmm) REVERT: k 256 TRP cc_start: 0.7983 (m-90) cc_final: 0.7468 (m-90) REVERT: k 420 MET cc_start: 0.7882 (ptp) cc_final: 0.7107 (ptp) REVERT: q 145 TYR cc_start: 0.7634 (m-10) cc_final: 0.7430 (m-10) REVERT: r 38 GLU cc_start: 0.7607 (pm20) cc_final: 0.6566 (pm20) REVERT: r 39 GLU cc_start: 0.7627 (mp0) cc_final: 0.6633 (pm20) outliers start: 175 outliers final: 104 residues processed: 644 average time/residue: 0.6365 time to fit residues: 734.9012 Evaluate side-chains 587 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 476 time to evaluate : 6.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1460 LEU Chi-restraints excluded: chain a residue 1704 VAL Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 2060 VAL Chi-restraints excluded: chain a residue 2063 LEU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain a residue 2171 MET Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 286 THR Chi-restraints excluded: chain b residue 345 LEU Chi-restraints excluded: chain b residue 398 ILE Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 523 GLN Chi-restraints excluded: chain b residue 545 SER Chi-restraints excluded: chain b residue 726 ASP Chi-restraints excluded: chain b residue 820 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 896 LEU Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1046 ILE Chi-restraints excluded: chain b residue 1062 SER Chi-restraints excluded: chain b residue 1104 LEU Chi-restraints excluded: chain b residue 1108 VAL Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1193 VAL Chi-restraints excluded: chain c residue 121 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 241 LEU Chi-restraints excluded: chain d residue 467 LEU Chi-restraints excluded: chain d residue 493 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 823 THR Chi-restraints excluded: chain d residue 842 VAL Chi-restraints excluded: chain d residue 865 VAL Chi-restraints excluded: chain e residue 187 ARG Chi-restraints excluded: chain e residue 477 LEU Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain e residue 746 TRP Chi-restraints excluded: chain f residue 105 VAL Chi-restraints excluded: chain f residue 116 ASN Chi-restraints excluded: chain f residue 219 CYS Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 529 VAL Chi-restraints excluded: chain f residue 554 ASP Chi-restraints excluded: chain f residue 559 MET Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 315 LEU Chi-restraints excluded: chain g residue 460 LEU Chi-restraints excluded: chain g residue 573 GLN Chi-restraints excluded: chain g residue 601 ILE Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 717 ILE Chi-restraints excluded: chain g residue 769 VAL Chi-restraints excluded: chain g residue 799 LEU Chi-restraints excluded: chain g residue 845 ARG Chi-restraints excluded: chain g residue 890 THR Chi-restraints excluded: chain g residue 894 LEU Chi-restraints excluded: chain g residue 905 THR Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 920 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 260 TYR Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 458 MET Chi-restraints excluded: chain h residue 489 ASN Chi-restraints excluded: chain h residue 717 LEU Chi-restraints excluded: chain h residue 741 LEU Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 936 THR Chi-restraints excluded: chain h residue 958 ILE Chi-restraints excluded: chain h residue 977 LEU Chi-restraints excluded: chain i residue 309 LEU Chi-restraints excluded: chain i residue 404 ASP Chi-restraints excluded: chain i residue 444 ILE Chi-restraints excluded: chain i residue 545 HIS Chi-restraints excluded: chain k residue 302 PHE Chi-restraints excluded: chain k residue 448 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 63 ASP Chi-restraints excluded: chain p residue 103 VAL Chi-restraints excluded: chain p residue 117 HIS Chi-restraints excluded: chain p residue 201 VAL Chi-restraints excluded: chain p residue 353 SER Chi-restraints excluded: chain p residue 430 LEU Chi-restraints excluded: chain p residue 439 PHE Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 86 TYR Chi-restraints excluded: chain q residue 113 ILE Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 202 ASP Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain q residue 278 LEU Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 52 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 805 optimal weight: 40.0000 chunk 549 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 720 optimal weight: 9.9990 chunk 399 optimal weight: 1.9990 chunk 825 optimal weight: 20.0000 chunk 668 optimal weight: 1.9990 chunk 1 optimal weight: 30.0000 chunk 494 optimal weight: 2.9990 chunk 868 optimal weight: 0.5980 chunk 244 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1666 HIS ** b 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 HIS b 381 HIS b 555 HIS ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 577 ASN ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 445 ASN ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 75427 Z= 0.215 Angle : 0.574 12.179 102722 Z= 0.282 Chirality : 0.039 0.404 12310 Planarity : 0.004 0.054 13256 Dihedral : 3.976 38.458 10640 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 2.32 % Allowed : 14.96 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 9922 helix: 1.93 (0.07), residues: 6442 sheet: -0.35 (0.25), residues: 449 loop : -0.72 (0.12), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP e 225 HIS 0.014 0.001 HIS p 304 PHE 0.037 0.001 PHE h 54 TYR 0.031 0.001 TYR b 486 ARG 0.006 0.000 ARG e 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 501 time to evaluate : 6.387 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: b 45 LEU cc_start: 0.8940 (mt) cc_final: 0.8628 (mm) REVERT: b 252 PHE cc_start: 0.8089 (m-10) cc_final: 0.7875 (m-80) REVERT: b 435 MET cc_start: 0.8521 (mmm) cc_final: 0.8151 (mmt) REVERT: b 479 MET cc_start: 0.8183 (ptm) cc_final: 0.7757 (tmm) REVERT: b 1128 ILE cc_start: 0.8581 (tt) cc_final: 0.8300 (tp) REVERT: d 111 MET cc_start: 0.9452 (ptp) cc_final: 0.9022 (ppp) REVERT: d 219 MET cc_start: 0.9084 (mmm) cc_final: 0.8834 (mmm) REVERT: d 725 MET cc_start: 0.8585 (tpp) cc_final: 0.8151 (mpp) REVERT: d 784 MET cc_start: 0.9205 (tpp) cc_final: 0.8421 (tpp) REVERT: d 874 MET cc_start: 0.8121 (ttt) cc_final: 0.7836 (ttt) REVERT: e 152 MET cc_start: 0.8320 (mmm) cc_final: 0.8014 (mmm) REVERT: e 181 MET cc_start: 0.4014 (mpt) cc_final: 0.3741 (mpt) REVERT: f 51 MET cc_start: 0.6859 (mmt) cc_final: 0.6218 (mmt) REVERT: f 91 SER cc_start: 0.8777 (m) cc_final: 0.8161 (t) REVERT: f 317 MET cc_start: 0.6793 (ptt) cc_final: 0.6219 (ptt) REVERT: f 434 MET cc_start: 0.5514 (mmt) cc_final: 0.4760 (mmm) REVERT: f 554 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7662 (t0) REVERT: g 102 GLU cc_start: 0.7895 (tp30) cc_final: 0.7495 (tp30) REVERT: g 275 ASP cc_start: 0.7705 (m-30) cc_final: 0.7351 (m-30) REVERT: g 450 CYS cc_start: 0.8921 (m) cc_final: 0.8465 (m) REVERT: g 541 MET cc_start: 0.7805 (tpp) cc_final: 0.7473 (tpp) REVERT: h 141 MET cc_start: 0.2172 (ptt) cc_final: 0.1941 (mtm) REVERT: i 25 MET cc_start: 0.8713 (tmm) cc_final: 0.8346 (tmm) REVERT: i 444 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8242 (mp) REVERT: k 30 MET cc_start: 0.6435 (tpp) cc_final: 0.6132 (tpp) REVERT: k 130 MET cc_start: 0.8625 (ttm) cc_final: 0.8122 (tpt) REVERT: k 181 MET cc_start: 0.8075 (mmm) cc_final: 0.7755 (mmm) REVERT: k 420 MET cc_start: 0.7889 (ptp) cc_final: 0.7126 (ptp) REVERT: p 85 TYR cc_start: 0.8823 (m-10) cc_final: 0.8597 (m-80) REVERT: q 122 GLN cc_start: 0.7625 (mp10) cc_final: 0.7423 (mp10) REVERT: r 38 GLU cc_start: 0.7597 (pm20) cc_final: 0.6552 (pm20) REVERT: r 39 GLU cc_start: 0.7621 (mp0) cc_final: 0.6601 (pm20) outliers start: 169 outliers final: 99 residues processed: 639 average time/residue: 0.6416 time to fit residues: 733.4318 Evaluate side-chains 574 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 473 time to evaluate : 6.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 1621 SER Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1460 LEU Chi-restraints excluded: chain a residue 1511 ARG Chi-restraints excluded: chain a residue 2060 VAL Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 480 LEU Chi-restraints excluded: chain b residue 523 GLN Chi-restraints excluded: chain b residue 703 LEU Chi-restraints excluded: chain b residue 726 ASP Chi-restraints excluded: chain b residue 820 LEU Chi-restraints excluded: chain b residue 858 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 896 LEU Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1046 ILE Chi-restraints excluded: chain b residue 1108 VAL Chi-restraints excluded: chain b residue 1121 ILE Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 241 LEU Chi-restraints excluded: chain d residue 467 LEU Chi-restraints excluded: chain d residue 493 LEU Chi-restraints excluded: chain d residue 685 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 691 ASP Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 842 VAL Chi-restraints excluded: chain d residue 865 VAL Chi-restraints excluded: chain e residue 187 ARG Chi-restraints excluded: chain e residue 409 PHE Chi-restraints excluded: chain e residue 477 LEU Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 506 LEU Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain e residue 746 TRP Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 105 VAL Chi-restraints excluded: chain f residue 219 CYS Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 529 VAL Chi-restraints excluded: chain f residue 554 ASP Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 176 ILE Chi-restraints excluded: chain g residue 315 LEU Chi-restraints excluded: chain g residue 460 LEU Chi-restraints excluded: chain g residue 470 ASP Chi-restraints excluded: chain g residue 692 SER Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 717 ILE Chi-restraints excluded: chain g residue 769 VAL Chi-restraints excluded: chain g residue 894 LEU Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 920 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 458 MET Chi-restraints excluded: chain h residue 489 ASN Chi-restraints excluded: chain h residue 530 ILE Chi-restraints excluded: chain h residue 611 MET Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 895 THR Chi-restraints excluded: chain h residue 906 GLU Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 958 ILE Chi-restraints excluded: chain h residue 977 LEU Chi-restraints excluded: chain i residue 309 LEU Chi-restraints excluded: chain i residue 436 TYR Chi-restraints excluded: chain i residue 444 ILE Chi-restraints excluded: chain i residue 486 MET Chi-restraints excluded: chain i residue 519 MET Chi-restraints excluded: chain i residue 545 HIS Chi-restraints excluded: chain k residue 302 PHE Chi-restraints excluded: chain k residue 448 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 63 ASP Chi-restraints excluded: chain p residue 117 HIS Chi-restraints excluded: chain p residue 201 VAL Chi-restraints excluded: chain p residue 329 CYS Chi-restraints excluded: chain p residue 353 SER Chi-restraints excluded: chain p residue 430 LEU Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 86 TYR Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 202 ASP Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain q residue 278 LEU Chi-restraints excluded: chain q residue 290 ASP Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 52 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 325 optimal weight: 0.8980 chunk 871 optimal weight: 5.9990 chunk 191 optimal weight: 0.2980 chunk 568 optimal weight: 4.9990 chunk 238 optimal weight: 40.0000 chunk 968 optimal weight: 0.9980 chunk 803 optimal weight: 9.9990 chunk 448 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 320 optimal weight: 0.4980 chunk 508 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 528 GLN ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 HIS ** p 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 340 HIS ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 75427 Z= 0.166 Angle : 0.571 15.246 102722 Z= 0.276 Chirality : 0.039 0.386 12310 Planarity : 0.004 0.055 13256 Dihedral : 3.876 37.558 10640 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 2.00 % Allowed : 15.45 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 9922 helix: 2.03 (0.07), residues: 6458 sheet: -0.20 (0.25), residues: 460 loop : -0.66 (0.12), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP k 256 HIS 0.007 0.001 HIS p 87 PHE 0.034 0.001 PHE h 54 TYR 0.026 0.001 TYR i 313 ARG 0.007 0.000 ARG e 733 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 519 time to evaluate : 6.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 2127 TYR cc_start: 0.8347 (t80) cc_final: 0.7447 (t80) REVERT: b 196 ASP cc_start: 0.7012 (t0) cc_final: 0.6740 (t70) REVERT: b 435 MET cc_start: 0.8518 (mmm) cc_final: 0.8141 (mmt) REVERT: b 479 MET cc_start: 0.8182 (ptm) cc_final: 0.7768 (tmm) REVERT: b 486 TYR cc_start: 0.7195 (m-80) cc_final: 0.6936 (m-80) REVERT: b 1128 ILE cc_start: 0.8559 (tt) cc_final: 0.8284 (tp) REVERT: d 111 MET cc_start: 0.9442 (ptp) cc_final: 0.9020 (ppp) REVERT: d 219 MET cc_start: 0.9086 (mmm) cc_final: 0.8874 (mmm) REVERT: d 725 MET cc_start: 0.8529 (tpp) cc_final: 0.8156 (mpp) REVERT: d 784 MET cc_start: 0.8981 (tpp) cc_final: 0.8371 (tpp) REVERT: e 152 MET cc_start: 0.8342 (mmm) cc_final: 0.8027 (mmm) REVERT: e 181 MET cc_start: 0.4483 (mpt) cc_final: 0.4055 (mpt) REVERT: e 190 MET cc_start: 0.4952 (mtp) cc_final: 0.4673 (mtp) REVERT: f 51 MET cc_start: 0.6639 (mmt) cc_final: 0.6211 (mmt) REVERT: f 91 SER cc_start: 0.8725 (m) cc_final: 0.8085 (t) REVERT: f 434 MET cc_start: 0.5400 (mmt) cc_final: 0.4733 (mmm) REVERT: f 554 ASP cc_start: 0.8223 (m-30) cc_final: 0.7620 (t0) REVERT: g 102 GLU cc_start: 0.7781 (tp30) cc_final: 0.7395 (tp30) REVERT: g 275 ASP cc_start: 0.7608 (m-30) cc_final: 0.7402 (m-30) REVERT: g 450 CYS cc_start: 0.9018 (m) cc_final: 0.8645 (m) REVERT: g 541 MET cc_start: 0.7708 (tpp) cc_final: 0.7361 (tpp) REVERT: h 141 MET cc_start: 0.2155 (ptt) cc_final: 0.1924 (mtt) REVERT: h 597 LEU cc_start: 0.8878 (pp) cc_final: 0.8483 (tp) REVERT: i 25 MET cc_start: 0.8692 (tmm) cc_final: 0.8363 (tmm) REVERT: i 312 LEU cc_start: 0.9516 (mt) cc_final: 0.9304 (mt) REVERT: i 444 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8286 (mp) REVERT: k 35 MET cc_start: 0.7831 (tmm) cc_final: 0.7265 (tmm) REVERT: k 130 MET cc_start: 0.8608 (ttm) cc_final: 0.8109 (tpt) REVERT: k 181 MET cc_start: 0.8130 (mmm) cc_final: 0.7837 (mmm) REVERT: k 420 MET cc_start: 0.7897 (ptp) cc_final: 0.7127 (ptp) REVERT: p 85 TYR cc_start: 0.8813 (m-10) cc_final: 0.8610 (m-80) REVERT: r 38 GLU cc_start: 0.7573 (pm20) cc_final: 0.6567 (pm20) REVERT: r 39 GLU cc_start: 0.7679 (mp0) cc_final: 0.6570 (pm20) REVERT: r 58 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6733 (ppp) outliers start: 146 outliers final: 92 residues processed: 627 average time/residue: 0.6393 time to fit residues: 717.6408 Evaluate side-chains 576 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 482 time to evaluate : 6.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1460 LEU Chi-restraints excluded: chain a residue 1511 ARG Chi-restraints excluded: chain a residue 1704 VAL Chi-restraints excluded: chain a residue 1884 ILE Chi-restraints excluded: chain a residue 2060 VAL Chi-restraints excluded: chain a residue 2063 LEU Chi-restraints excluded: chain a residue 2159 LEU Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 345 LEU Chi-restraints excluded: chain b residue 480 LEU Chi-restraints excluded: chain b residue 523 GLN Chi-restraints excluded: chain b residue 703 LEU Chi-restraints excluded: chain b residue 764 VAL Chi-restraints excluded: chain b residue 820 LEU Chi-restraints excluded: chain b residue 858 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1104 LEU Chi-restraints excluded: chain b residue 1180 ASP Chi-restraints excluded: chain b residue 1193 VAL Chi-restraints excluded: chain c residue 121 ILE Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 241 LEU Chi-restraints excluded: chain d residue 493 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 842 VAL Chi-restraints excluded: chain d residue 865 VAL Chi-restraints excluded: chain e residue 187 ARG Chi-restraints excluded: chain e residue 409 PHE Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain e residue 746 TRP Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 105 VAL Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 332 SER Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 176 ILE Chi-restraints excluded: chain g residue 315 LEU Chi-restraints excluded: chain g residue 460 LEU Chi-restraints excluded: chain g residue 470 ASP Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 769 VAL Chi-restraints excluded: chain g residue 784 LEU Chi-restraints excluded: chain g residue 894 LEU Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 920 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 458 MET Chi-restraints excluded: chain h residue 489 ASN Chi-restraints excluded: chain h residue 530 ILE Chi-restraints excluded: chain h residue 741 LEU Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 906 GLU Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 977 LEU Chi-restraints excluded: chain i residue 309 LEU Chi-restraints excluded: chain i residue 404 ASP Chi-restraints excluded: chain i residue 436 TYR Chi-restraints excluded: chain i residue 444 ILE Chi-restraints excluded: chain i residue 486 MET Chi-restraints excluded: chain i residue 519 MET Chi-restraints excluded: chain i residue 545 HIS Chi-restraints excluded: chain k residue 448 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 63 ASP Chi-restraints excluded: chain p residue 103 VAL Chi-restraints excluded: chain p residue 117 HIS Chi-restraints excluded: chain p residue 201 VAL Chi-restraints excluded: chain p residue 353 SER Chi-restraints excluded: chain p residue 430 LEU Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 86 TYR Chi-restraints excluded: chain q residue 113 ILE Chi-restraints excluded: chain q residue 202 ASP Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain q residue 290 ASP Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 58 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 933 optimal weight: 40.0000 chunk 109 optimal weight: 1.9990 chunk 551 optimal weight: 0.0000 chunk 707 optimal weight: 2.9990 chunk 547 optimal weight: 2.9990 chunk 815 optimal weight: 9.9990 chunk 540 optimal weight: 2.9990 chunk 964 optimal weight: 0.9990 chunk 603 optimal weight: 5.9990 chunk 588 optimal weight: 1.9990 chunk 445 optimal weight: 0.4980 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 HIS ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 75427 Z= 0.202 Angle : 0.576 14.158 102722 Z= 0.279 Chirality : 0.039 0.439 12310 Planarity : 0.004 0.060 13256 Dihedral : 3.837 37.442 10640 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 2.05 % Allowed : 15.76 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 9922 helix: 2.04 (0.07), residues: 6467 sheet: -0.14 (0.25), residues: 457 loop : -0.65 (0.12), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP k 576 HIS 0.007 0.001 HIS p 87 PHE 0.030 0.001 PHE h 54 TYR 0.019 0.001 TYR e 774 ARG 0.007 0.000 ARG e 733 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 501 time to evaluate : 6.504 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 2127 TYR cc_start: 0.8346 (t80) cc_final: 0.7440 (t80) REVERT: b 435 MET cc_start: 0.8477 (mmm) cc_final: 0.8173 (mmt) REVERT: b 479 MET cc_start: 0.8256 (ptm) cc_final: 0.7853 (tmm) REVERT: b 710 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8850 (mp) REVERT: b 1128 ILE cc_start: 0.8528 (tt) cc_final: 0.8249 (tp) REVERT: d 111 MET cc_start: 0.9434 (ptp) cc_final: 0.9017 (ppp) REVERT: d 219 MET cc_start: 0.9109 (mmm) cc_final: 0.8903 (mmm) REVERT: d 256 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9048 (tt) REVERT: d 400 MET cc_start: 0.8302 (mpp) cc_final: 0.8026 (mpp) REVERT: d 725 MET cc_start: 0.8571 (tpp) cc_final: 0.8175 (mpp) REVERT: e 152 MET cc_start: 0.8379 (mmm) cc_final: 0.7956 (mmt) REVERT: e 181 MET cc_start: 0.4543 (mpt) cc_final: 0.3698 (mpt) REVERT: e 190 MET cc_start: 0.5130 (mtp) cc_final: 0.4475 (mtp) REVERT: f 104 LEU cc_start: 0.8832 (mm) cc_final: 0.8616 (mt) REVERT: f 434 MET cc_start: 0.5376 (mmt) cc_final: 0.4828 (mmm) REVERT: f 554 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7650 (t0) REVERT: g 102 GLU cc_start: 0.7826 (tp30) cc_final: 0.7421 (tp30) REVERT: g 275 ASP cc_start: 0.7625 (m-30) cc_final: 0.7386 (m-30) REVERT: g 443 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7410 (p0) REVERT: g 450 CYS cc_start: 0.9039 (m) cc_final: 0.8675 (m) REVERT: g 489 LEU cc_start: 0.9421 (tp) cc_final: 0.9164 (tt) REVERT: g 541 MET cc_start: 0.7763 (tpp) cc_final: 0.7437 (tpp) REVERT: g 677 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7638 (mm-30) REVERT: h 597 LEU cc_start: 0.8875 (pp) cc_final: 0.8469 (tp) REVERT: i 25 MET cc_start: 0.8641 (tmm) cc_final: 0.8303 (tmm) REVERT: i 312 LEU cc_start: 0.9508 (mt) cc_final: 0.9305 (mt) REVERT: i 444 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8275 (mp) REVERT: k 35 MET cc_start: 0.7833 (tmm) cc_final: 0.7304 (tmm) REVERT: k 130 MET cc_start: 0.8613 (ttm) cc_final: 0.8070 (tpt) REVERT: k 181 MET cc_start: 0.8175 (mmm) cc_final: 0.7864 (mmm) REVERT: k 420 MET cc_start: 0.7908 (ptp) cc_final: 0.7029 (ptp) REVERT: p 85 TYR cc_start: 0.8795 (m-80) cc_final: 0.8590 (m-80) REVERT: r 38 GLU cc_start: 0.7655 (pm20) cc_final: 0.6690 (pm20) REVERT: r 39 GLU cc_start: 0.7723 (mp0) cc_final: 0.6603 (pm20) REVERT: r 58 MET cc_start: 0.7419 (ppp) cc_final: 0.6831 (ppp) outliers start: 149 outliers final: 108 residues processed: 630 average time/residue: 0.6418 time to fit residues: 724.7757 Evaluate side-chains 582 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 469 time to evaluate : 6.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain Y residue 1621 SER Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1460 LEU Chi-restraints excluded: chain a residue 1511 ARG Chi-restraints excluded: chain a residue 1704 VAL Chi-restraints excluded: chain a residue 2060 VAL Chi-restraints excluded: chain a residue 2063 LEU Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 480 LEU Chi-restraints excluded: chain b residue 523 GLN Chi-restraints excluded: chain b residue 545 SER Chi-restraints excluded: chain b residue 703 LEU Chi-restraints excluded: chain b residue 710 LEU Chi-restraints excluded: chain b residue 820 LEU Chi-restraints excluded: chain b residue 858 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 881 LEU Chi-restraints excluded: chain b residue 896 LEU Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1046 ILE Chi-restraints excluded: chain b residue 1104 LEU Chi-restraints excluded: chain b residue 1108 VAL Chi-restraints excluded: chain b residue 1121 ILE Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1180 ASP Chi-restraints excluded: chain b residue 1193 VAL Chi-restraints excluded: chain c residue 121 ILE Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 241 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 482 ILE Chi-restraints excluded: chain d residue 493 LEU Chi-restraints excluded: chain d residue 685 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 691 ASP Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 842 VAL Chi-restraints excluded: chain d residue 865 VAL Chi-restraints excluded: chain e residue 187 ARG Chi-restraints excluded: chain e residue 409 PHE Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain e residue 746 TRP Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 105 VAL Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 332 SER Chi-restraints excluded: chain f residue 529 VAL Chi-restraints excluded: chain f residue 554 ASP Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 176 ILE Chi-restraints excluded: chain g residue 315 LEU Chi-restraints excluded: chain g residue 443 ASP Chi-restraints excluded: chain g residue 460 LEU Chi-restraints excluded: chain g residue 470 ASP Chi-restraints excluded: chain g residue 601 ILE Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 769 VAL Chi-restraints excluded: chain g residue 784 LEU Chi-restraints excluded: chain g residue 894 LEU Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 920 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 458 MET Chi-restraints excluded: chain h residue 489 ASN Chi-restraints excluded: chain h residue 530 ILE Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 895 THR Chi-restraints excluded: chain h residue 906 GLU Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 958 ILE Chi-restraints excluded: chain h residue 977 LEU Chi-restraints excluded: chain i residue 309 LEU Chi-restraints excluded: chain i residue 404 ASP Chi-restraints excluded: chain i residue 444 ILE Chi-restraints excluded: chain i residue 486 MET Chi-restraints excluded: chain i residue 519 MET Chi-restraints excluded: chain i residue 545 HIS Chi-restraints excluded: chain k residue 302 PHE Chi-restraints excluded: chain k residue 448 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 63 ASP Chi-restraints excluded: chain p residue 103 VAL Chi-restraints excluded: chain p residue 117 HIS Chi-restraints excluded: chain p residue 201 VAL Chi-restraints excluded: chain p residue 353 SER Chi-restraints excluded: chain p residue 430 LEU Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 86 TYR Chi-restraints excluded: chain q residue 113 ILE Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 202 ASP Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain q residue 278 LEU Chi-restraints excluded: chain q residue 290 ASP Chi-restraints excluded: chain r residue 36 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 596 optimal weight: 0.9990 chunk 385 optimal weight: 3.9990 chunk 576 optimal weight: 0.7980 chunk 290 optimal weight: 0.9990 chunk 189 optimal weight: 0.4980 chunk 186 optimal weight: 0.6980 chunk 613 optimal weight: 3.9990 chunk 657 optimal weight: 1.9990 chunk 477 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 758 optimal weight: 50.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 72 ASN ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 288 GLN ** p 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 75427 Z= 0.176 Angle : 0.582 14.460 102722 Z= 0.280 Chirality : 0.039 0.412 12310 Planarity : 0.004 0.059 13256 Dihedral : 3.807 37.325 10640 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.39 % Rotamer: Outliers : 1.89 % Allowed : 16.26 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.09), residues: 9922 helix: 2.07 (0.07), residues: 6467 sheet: -0.05 (0.24), residues: 468 loop : -0.63 (0.12), residues: 2987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP e 225 HIS 0.006 0.001 HIS p 87 PHE 0.029 0.001 PHE h 54 TYR 0.021 0.001 TYR d 55 ARG 0.005 0.000 ARG e 733 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 496 time to evaluate : 6.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 2127 TYR cc_start: 0.8319 (t80) cc_final: 0.7422 (t80) REVERT: b 479 MET cc_start: 0.8234 (ptm) cc_final: 0.7837 (tmm) REVERT: b 710 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8857 (mp) REVERT: b 743 MET cc_start: 0.8606 (tpp) cc_final: 0.8079 (tpp) REVERT: b 1128 ILE cc_start: 0.8516 (tt) cc_final: 0.8226 (tp) REVERT: d 111 MET cc_start: 0.9404 (ptp) cc_final: 0.9012 (ppp) REVERT: d 219 MET cc_start: 0.9111 (mmm) cc_final: 0.8899 (mmm) REVERT: d 256 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9056 (tt) REVERT: d 725 MET cc_start: 0.8544 (tpp) cc_final: 0.8175 (mpp) REVERT: e 152 MET cc_start: 0.8371 (mmm) cc_final: 0.7982 (mmt) REVERT: e 181 MET cc_start: 0.4458 (mpt) cc_final: 0.4012 (mpt) REVERT: e 190 MET cc_start: 0.5007 (mtp) cc_final: 0.4610 (mtp) REVERT: f 104 LEU cc_start: 0.8846 (mm) cc_final: 0.8628 (mt) REVERT: f 434 MET cc_start: 0.5479 (mmt) cc_final: 0.4907 (mmm) REVERT: f 554 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7602 (t0) REVERT: g 102 GLU cc_start: 0.7790 (tp30) cc_final: 0.7438 (tp30) REVERT: g 443 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7526 (p0) REVERT: g 450 CYS cc_start: 0.9080 (m) cc_final: 0.8601 (m) REVERT: g 541 MET cc_start: 0.7726 (tpp) cc_final: 0.7389 (tpp) REVERT: g 677 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7594 (mm-30) REVERT: h 597 LEU cc_start: 0.8908 (pp) cc_final: 0.8461 (tp) REVERT: i 25 MET cc_start: 0.8638 (tmm) cc_final: 0.8364 (tmm) REVERT: i 312 LEU cc_start: 0.9510 (mt) cc_final: 0.9306 (mt) REVERT: i 444 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8273 (mp) REVERT: k 35 MET cc_start: 0.7872 (tmm) cc_final: 0.7301 (tmm) REVERT: k 92 MET cc_start: 0.6866 (tmm) cc_final: 0.6232 (tmm) REVERT: k 130 MET cc_start: 0.8610 (ttm) cc_final: 0.8077 (tpt) REVERT: k 181 MET cc_start: 0.8216 (mmm) cc_final: 0.7886 (mmm) REVERT: k 420 MET cc_start: 0.7908 (ptp) cc_final: 0.6997 (ptp) REVERT: q 175 ASP cc_start: 0.7222 (p0) cc_final: 0.6948 (p0) REVERT: r 38 GLU cc_start: 0.7659 (pm20) cc_final: 0.6676 (pm20) REVERT: r 39 GLU cc_start: 0.7723 (mp0) cc_final: 0.6589 (pm20) REVERT: r 58 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6815 (ppp) outliers start: 138 outliers final: 105 residues processed: 614 average time/residue: 0.6287 time to fit residues: 692.4182 Evaluate side-chains 589 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 478 time to evaluate : 6.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 1621 SER Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1460 LEU Chi-restraints excluded: chain a residue 1511 ARG Chi-restraints excluded: chain a residue 1704 VAL Chi-restraints excluded: chain a residue 2060 VAL Chi-restraints excluded: chain a residue 2063 LEU Chi-restraints excluded: chain a residue 2080 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 480 LEU Chi-restraints excluded: chain b residue 523 GLN Chi-restraints excluded: chain b residue 703 LEU Chi-restraints excluded: chain b residue 710 LEU Chi-restraints excluded: chain b residue 764 VAL Chi-restraints excluded: chain b residue 858 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 877 THR Chi-restraints excluded: chain b residue 896 LEU Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1062 SER Chi-restraints excluded: chain b residue 1104 LEU Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1140 THR Chi-restraints excluded: chain b residue 1180 ASP Chi-restraints excluded: chain b residue 1193 VAL Chi-restraints excluded: chain c residue 121 ILE Chi-restraints excluded: chain c residue 191 LEU Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 241 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 482 ILE Chi-restraints excluded: chain d residue 493 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 691 ASP Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 823 THR Chi-restraints excluded: chain d residue 842 VAL Chi-restraints excluded: chain e residue 187 ARG Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 506 LEU Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain e residue 746 TRP Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 105 VAL Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 332 SER Chi-restraints excluded: chain f residue 529 VAL Chi-restraints excluded: chain f residue 554 ASP Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 176 ILE Chi-restraints excluded: chain g residue 232 ILE Chi-restraints excluded: chain g residue 315 LEU Chi-restraints excluded: chain g residue 443 ASP Chi-restraints excluded: chain g residue 449 MET Chi-restraints excluded: chain g residue 460 LEU Chi-restraints excluded: chain g residue 470 ASP Chi-restraints excluded: chain g residue 601 ILE Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 769 VAL Chi-restraints excluded: chain g residue 784 LEU Chi-restraints excluded: chain g residue 894 LEU Chi-restraints excluded: chain g residue 905 THR Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 920 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 256 LEU Chi-restraints excluded: chain h residue 263 GLN Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 458 MET Chi-restraints excluded: chain h residue 489 ASN Chi-restraints excluded: chain h residue 530 ILE Chi-restraints excluded: chain h residue 741 LEU Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 895 THR Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 977 LEU Chi-restraints excluded: chain i residue 309 LEU Chi-restraints excluded: chain i residue 404 ASP Chi-restraints excluded: chain i residue 444 ILE Chi-restraints excluded: chain i residue 486 MET Chi-restraints excluded: chain i residue 519 MET Chi-restraints excluded: chain i residue 545 HIS Chi-restraints excluded: chain k residue 448 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 103 VAL Chi-restraints excluded: chain p residue 201 VAL Chi-restraints excluded: chain p residue 353 SER Chi-restraints excluded: chain p residue 430 LEU Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 113 ILE Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 202 ASP Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain q residue 278 LEU Chi-restraints excluded: chain q residue 290 ASP Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 58 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 877 optimal weight: 9.9990 chunk 924 optimal weight: 7.9990 chunk 843 optimal weight: 40.0000 chunk 899 optimal weight: 9.9990 chunk 541 optimal weight: 0.4980 chunk 391 optimal weight: 7.9990 chunk 705 optimal weight: 40.0000 chunk 275 optimal weight: 20.0000 chunk 812 optimal weight: 0.5980 chunk 850 optimal weight: 5.9990 chunk 895 optimal weight: 50.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1904 HIS ** b 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 751 ASN c 72 ASN ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 452 HIS e 698 HIS e 888 HIS e 894 HIS ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 GLN f 265 HIS f 363 HIS g 563 ASN ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 922 HIS ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 GLN ** p 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 75427 Z= 0.597 Angle : 0.777 11.868 102722 Z= 0.387 Chirality : 0.047 0.430 12310 Planarity : 0.005 0.112 13256 Dihedral : 4.307 41.502 10640 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 2.14 % Allowed : 16.52 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 9922 helix: 1.58 (0.07), residues: 6453 sheet: -0.32 (0.25), residues: 461 loop : -0.85 (0.12), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 902 HIS 0.015 0.002 HIS d 568 PHE 0.031 0.002 PHE h 54 TYR 0.033 0.002 TYR e 193 ARG 0.014 0.001 ARG e 733 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 476 time to evaluate : 6.699 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 2111 MET cc_start: 0.7918 (ttm) cc_final: 0.7619 (ttm) REVERT: b 479 MET cc_start: 0.8433 (ptm) cc_final: 0.7944 (tmm) REVERT: b 1104 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8355 (mp) REVERT: b 1128 ILE cc_start: 0.8628 (tt) cc_final: 0.8371 (tp) REVERT: d 111 MET cc_start: 0.9423 (ptp) cc_final: 0.9024 (ppp) REVERT: d 219 MET cc_start: 0.9216 (mmm) cc_final: 0.8973 (mmm) REVERT: d 256 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9115 (tt) REVERT: d 784 MET cc_start: 0.9450 (tpp) cc_final: 0.9184 (tpp) REVERT: e 181 MET cc_start: 0.4335 (mpt) cc_final: 0.3852 (mpt) REVERT: e 190 MET cc_start: 0.5144 (mtp) cc_final: 0.4792 (mtp) REVERT: f 51 MET cc_start: 0.6920 (mmt) cc_final: 0.6215 (mmt) REVERT: f 91 SER cc_start: 0.9020 (m) cc_final: 0.8289 (t) REVERT: f 434 MET cc_start: 0.5441 (mmt) cc_final: 0.4938 (mmm) REVERT: f 554 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7863 (t0) REVERT: g 59 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8070 (tp) REVERT: g 275 ASP cc_start: 0.7776 (m-30) cc_final: 0.7214 (t0) REVERT: g 443 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7555 (p0) REVERT: g 450 CYS cc_start: 0.9063 (m) cc_final: 0.8671 (m) REVERT: g 541 MET cc_start: 0.8098 (tpp) cc_final: 0.7804 (tpp) REVERT: h 597 LEU cc_start: 0.9011 (pp) cc_final: 0.8537 (tt) REVERT: i 25 MET cc_start: 0.8554 (tmm) cc_final: 0.7985 (tmm) REVERT: i 137 MET cc_start: 0.7858 (mpp) cc_final: 0.7509 (mpp) REVERT: i 312 LEU cc_start: 0.9539 (mt) cc_final: 0.9331 (mt) REVERT: i 444 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8420 (mp) REVERT: k 35 MET cc_start: 0.8031 (tmm) cc_final: 0.7499 (tmm) REVERT: k 130 MET cc_start: 0.8516 (ttm) cc_final: 0.7926 (tpt) REVERT: k 181 MET cc_start: 0.8285 (mmm) cc_final: 0.7905 (mmm) REVERT: k 289 LYS cc_start: 0.6400 (tttp) cc_final: 0.5749 (tmtt) REVERT: k 420 MET cc_start: 0.7974 (ptp) cc_final: 0.7087 (ptp) REVERT: q 178 ASP cc_start: 0.8243 (m-30) cc_final: 0.8021 (m-30) outliers start: 156 outliers final: 111 residues processed: 608 average time/residue: 0.6354 time to fit residues: 691.6025 Evaluate side-chains 564 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 447 time to evaluate : 6.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain Y residue 1621 SER Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1460 LEU Chi-restraints excluded: chain a residue 1511 ARG Chi-restraints excluded: chain a residue 1704 VAL Chi-restraints excluded: chain a residue 1727 VAL Chi-restraints excluded: chain a residue 2060 VAL Chi-restraints excluded: chain a residue 2063 LEU Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 345 LEU Chi-restraints excluded: chain b residue 523 GLN Chi-restraints excluded: chain b residue 544 LEU Chi-restraints excluded: chain b residue 545 SER Chi-restraints excluded: chain b residue 764 VAL Chi-restraints excluded: chain b residue 820 LEU Chi-restraints excluded: chain b residue 858 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 877 THR Chi-restraints excluded: chain b residue 896 LEU Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1062 SER Chi-restraints excluded: chain b residue 1104 LEU Chi-restraints excluded: chain b residue 1108 VAL Chi-restraints excluded: chain b residue 1121 ILE Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1140 THR Chi-restraints excluded: chain b residue 1180 ASP Chi-restraints excluded: chain b residue 1193 VAL Chi-restraints excluded: chain c residue 121 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 241 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 482 ILE Chi-restraints excluded: chain d residue 493 LEU Chi-restraints excluded: chain d residue 685 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 823 THR Chi-restraints excluded: chain d residue 842 VAL Chi-restraints excluded: chain d residue 865 VAL Chi-restraints excluded: chain e residue 187 ARG Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 506 LEU Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain e residue 746 TRP Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 105 VAL Chi-restraints excluded: chain f residue 219 CYS Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 332 SER Chi-restraints excluded: chain f residue 529 VAL Chi-restraints excluded: chain f residue 554 ASP Chi-restraints excluded: chain f residue 561 SER Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 66 LEU Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 315 LEU Chi-restraints excluded: chain g residue 443 ASP Chi-restraints excluded: chain g residue 449 MET Chi-restraints excluded: chain g residue 460 LEU Chi-restraints excluded: chain g residue 470 ASP Chi-restraints excluded: chain g residue 553 VAL Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 769 VAL Chi-restraints excluded: chain g residue 849 SER Chi-restraints excluded: chain g residue 894 LEU Chi-restraints excluded: chain g residue 905 THR Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 920 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 256 LEU Chi-restraints excluded: chain h residue 260 TYR Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 458 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 496 THR Chi-restraints excluded: chain h residue 530 ILE Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 895 THR Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 958 ILE Chi-restraints excluded: chain h residue 977 LEU Chi-restraints excluded: chain i residue 309 LEU Chi-restraints excluded: chain i residue 404 ASP Chi-restraints excluded: chain i residue 444 ILE Chi-restraints excluded: chain i residue 519 MET Chi-restraints excluded: chain i residue 545 HIS Chi-restraints excluded: chain k residue 448 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 103 VAL Chi-restraints excluded: chain p residue 117 HIS Chi-restraints excluded: chain p residue 201 VAL Chi-restraints excluded: chain p residue 353 SER Chi-restraints excluded: chain p residue 430 LEU Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 495 TYR Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 86 TYR Chi-restraints excluded: chain q residue 113 ILE Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain q residue 278 LEU Chi-restraints excluded: chain q residue 290 ASP Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 590 optimal weight: 30.0000 chunk 950 optimal weight: 2.9990 chunk 580 optimal weight: 9.9990 chunk 451 optimal weight: 1.9990 chunk 660 optimal weight: 0.7980 chunk 997 optimal weight: 0.0000 chunk 917 optimal weight: 0.9990 chunk 794 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 613 optimal weight: 0.6980 chunk 486 optimal weight: 7.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 698 HIS ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 GLN ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 75427 Z= 0.199 Angle : 0.623 14.595 102722 Z= 0.301 Chirality : 0.040 0.411 12310 Planarity : 0.004 0.056 13256 Dihedral : 4.021 38.895 10640 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 1.55 % Allowed : 17.35 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 9922 helix: 1.86 (0.07), residues: 6466 sheet: -0.18 (0.25), residues: 467 loop : -0.67 (0.12), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP e 225 HIS 0.006 0.001 HIS d 289 PHE 0.023 0.001 PHE a1186 TYR 0.031 0.001 TYR p 169 ARG 0.012 0.000 ARG m 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19844 Ramachandran restraints generated. 9922 Oldfield, 0 Emsley, 9922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 482 time to evaluate : 6.550 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: b 479 MET cc_start: 0.8345 (ptm) cc_final: 0.7807 (tmm) REVERT: b 1128 ILE cc_start: 0.8473 (tt) cc_final: 0.8205 (tp) REVERT: d 111 MET cc_start: 0.9407 (ptp) cc_final: 0.9009 (ppp) REVERT: d 219 MET cc_start: 0.9147 (mmm) cc_final: 0.8889 (mmm) REVERT: d 256 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9061 (tt) REVERT: d 725 MET cc_start: 0.8582 (tpp) cc_final: 0.8024 (mpp) REVERT: e 181 MET cc_start: 0.4469 (mpt) cc_final: 0.4115 (mpt) REVERT: e 190 MET cc_start: 0.5228 (mtp) cc_final: 0.4769 (mtp) REVERT: f 51 MET cc_start: 0.6765 (mmt) cc_final: 0.6158 (mmt) REVERT: f 393 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7592 (pp) REVERT: f 434 MET cc_start: 0.5407 (mmt) cc_final: 0.4839 (mmm) REVERT: f 554 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7669 (t0) REVERT: g 59 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7887 (tp) REVERT: g 275 ASP cc_start: 0.7691 (m-30) cc_final: 0.7181 (t0) REVERT: g 437 GLN cc_start: 0.8284 (mm110) cc_final: 0.7958 (mm110) REVERT: g 443 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7489 (p0) REVERT: g 450 CYS cc_start: 0.9078 (m) cc_final: 0.8595 (m) REVERT: g 541 MET cc_start: 0.7875 (tpp) cc_final: 0.7572 (tpp) REVERT: g 677 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7743 (mm-30) REVERT: h 597 LEU cc_start: 0.8907 (pp) cc_final: 0.8482 (tp) REVERT: i 137 MET cc_start: 0.8006 (mpp) cc_final: 0.7693 (mpp) REVERT: i 444 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8359 (mp) REVERT: k 35 MET cc_start: 0.7944 (tmm) cc_final: 0.7406 (tmm) REVERT: k 92 MET cc_start: 0.7160 (tmm) cc_final: 0.6621 (tmm) REVERT: k 130 MET cc_start: 0.8591 (ttm) cc_final: 0.8067 (tpt) REVERT: k 420 MET cc_start: 0.7894 (ptp) cc_final: 0.6974 (ptp) REVERT: q 175 ASP cc_start: 0.7170 (p0) cc_final: 0.6938 (p0) REVERT: r 38 GLU cc_start: 0.7952 (pm20) cc_final: 0.7712 (pm20) REVERT: r 58 MET cc_start: 0.7807 (ppp) cc_final: 0.7168 (ptp) outliers start: 113 outliers final: 97 residues processed: 579 average time/residue: 0.6283 time to fit residues: 651.9847 Evaluate side-chains 565 residues out of total 8916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 462 time to evaluate : 6.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain Y residue 1621 SER Chi-restraints excluded: chain a residue 1305 HIS Chi-restraints excluded: chain a residue 1460 LEU Chi-restraints excluded: chain a residue 1704 VAL Chi-restraints excluded: chain a residue 1727 VAL Chi-restraints excluded: chain a residue 2060 VAL Chi-restraints excluded: chain a residue 2063 LEU Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 523 GLN Chi-restraints excluded: chain b residue 544 LEU Chi-restraints excluded: chain b residue 545 SER Chi-restraints excluded: chain b residue 764 VAL Chi-restraints excluded: chain b residue 820 LEU Chi-restraints excluded: chain b residue 858 LEU Chi-restraints excluded: chain b residue 867 VAL Chi-restraints excluded: chain b residue 877 THR Chi-restraints excluded: chain b residue 896 LEU Chi-restraints excluded: chain b residue 1027 LEU Chi-restraints excluded: chain b residue 1042 ILE Chi-restraints excluded: chain b residue 1062 SER Chi-restraints excluded: chain b residue 1108 VAL Chi-restraints excluded: chain b residue 1121 ILE Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1140 THR Chi-restraints excluded: chain b residue 1180 ASP Chi-restraints excluded: chain b residue 1193 VAL Chi-restraints excluded: chain c residue 121 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 482 ILE Chi-restraints excluded: chain d residue 493 LEU Chi-restraints excluded: chain d residue 687 LEU Chi-restraints excluded: chain d residue 704 THR Chi-restraints excluded: chain d residue 799 LEU Chi-restraints excluded: chain d residue 817 ILE Chi-restraints excluded: chain d residue 823 THR Chi-restraints excluded: chain d residue 842 VAL Chi-restraints excluded: chain d residue 865 VAL Chi-restraints excluded: chain e residue 187 ARG Chi-restraints excluded: chain e residue 477 LEU Chi-restraints excluded: chain e residue 502 LEU Chi-restraints excluded: chain e residue 506 LEU Chi-restraints excluded: chain e residue 645 LEU Chi-restraints excluded: chain e residue 746 TRP Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 105 VAL Chi-restraints excluded: chain f residue 227 VAL Chi-restraints excluded: chain f residue 270 VAL Chi-restraints excluded: chain f residue 332 SER Chi-restraints excluded: chain f residue 393 LEU Chi-restraints excluded: chain f residue 554 ASP Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 315 LEU Chi-restraints excluded: chain g residue 443 ASP Chi-restraints excluded: chain g residue 449 MET Chi-restraints excluded: chain g residue 460 LEU Chi-restraints excluded: chain g residue 470 ASP Chi-restraints excluded: chain g residue 694 ASP Chi-restraints excluded: chain g residue 769 VAL Chi-restraints excluded: chain g residue 894 LEU Chi-restraints excluded: chain g residue 905 THR Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain g residue 920 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain h residue 250 CYS Chi-restraints excluded: chain h residue 256 LEU Chi-restraints excluded: chain h residue 263 GLN Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 407 PHE Chi-restraints excluded: chain h residue 458 MET Chi-restraints excluded: chain h residue 530 ILE Chi-restraints excluded: chain h residue 762 LYS Chi-restraints excluded: chain h residue 895 THR Chi-restraints excluded: chain h residue 930 ASP Chi-restraints excluded: chain h residue 958 ILE Chi-restraints excluded: chain h residue 977 LEU Chi-restraints excluded: chain i residue 309 LEU Chi-restraints excluded: chain i residue 404 ASP Chi-restraints excluded: chain i residue 436 TYR Chi-restraints excluded: chain i residue 444 ILE Chi-restraints excluded: chain i residue 519 MET Chi-restraints excluded: chain i residue 545 HIS Chi-restraints excluded: chain k residue 448 THR Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 353 SER Chi-restraints excluded: chain p residue 430 LEU Chi-restraints excluded: chain p residue 447 CYS Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 83 MET Chi-restraints excluded: chain q residue 86 TYR Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 257 VAL Chi-restraints excluded: chain q residue 290 ASP Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1001 random chunks: chunk 630 optimal weight: 2.9990 chunk 845 optimal weight: 50.0000 chunk 243 optimal weight: 5.9990 chunk 732 optimal weight: 30.0000 chunk 117 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 795 optimal weight: 10.0000 chunk 332 optimal weight: 0.8980 chunk 816 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 146 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 480 GLN ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.140425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.117598 restraints weight = 234734.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.112694 restraints weight = 351180.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.110264 restraints weight = 248180.329| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 75427 Z= 0.197 Angle : 0.614 15.590 102722 Z= 0.294 Chirality : 0.040 0.380 12310 Planarity : 0.004 0.059 13256 Dihedral : 3.906 37.599 10640 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 1.70 % Allowed : 17.31 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.09), residues: 9922 helix: 1.96 (0.07), residues: 6469 sheet: -0.11 (0.25), residues: 470 loop : -0.60 (0.12), residues: 2983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 225 HIS 0.007 0.001 HIS d 289 PHE 0.035 0.001 PHE a1186 TYR 0.027 0.001 TYR e 774 ARG 0.015 0.000 ARG m 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14105.94 seconds wall clock time: 249 minutes 18.70 seconds (14958.70 seconds total)