Starting phenix.real_space_refine on Wed Feb 21 01:27:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py3_13709/02_2024/7py3_13709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py3_13709/02_2024/7py3_13709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py3_13709/02_2024/7py3_13709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py3_13709/02_2024/7py3_13709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py3_13709/02_2024/7py3_13709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py3_13709/02_2024/7py3_13709.pdb" } resolution = 3.8 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= 0.006 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 68 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 18090 2.51 5 N 5265 2.21 5 O 5831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 963": "OE1" <-> "OE2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1274": "OE1" <-> "OE2" Residue "C TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1321": "OE1" <-> "OE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29362 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "B" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2076 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 56, 'TRANS': 1282} Chain: "D" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10375 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 42, 'PHE:plan': 14, 'GLU:plan': 56, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 830 Chain: "N" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14877 SG CYS D 70 81.855 36.090 89.479 1.00155.50 S ATOM 14891 SG CYS D 72 82.055 32.908 91.677 1.00162.97 S ATOM 15023 SG CYS D 88 83.060 35.046 93.686 1.00154.73 S ATOM 21276 SG CYS D 888 91.951 100.742 103.503 1.00108.58 S ATOM 21327 SG CYS D 895 88.541 99.695 102.203 1.00101.00 S ATOM 21348 SG CYS D 898 91.085 103.285 101.485 1.00 99.07 S Time building chain proxies: 17.03, per 1000 atoms: 0.58 Number of scatterers: 29362 At special positions: 0 Unit cell: (186.39, 154.78, 179.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 105 16.00 P 68 15.00 Mg 1 11.99 O 5831 8.00 N 5265 7.00 C 18090 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: 12.18 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7018 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 45 sheets defined 37.0% alpha, 12.5% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 9.53 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.758A pdb=" N GLY A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.994A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 48 removed outlier: 3.860A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.415A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.142A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.538A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.511A pdb=" N ASP B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.601A pdb=" N SER B 266 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 296 through 308 removed outlier: 4.215A pdb=" N THR B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 removed outlier: 3.966A pdb=" N ALA B 327 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 40 removed outlier: 3.663A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.558A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.590A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.708A pdb=" N ARG C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.567A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.501A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.259A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.647A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.357A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.569A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 removed outlier: 4.100A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.798A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.777A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.961A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 907 removed outlier: 4.358A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.702A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.819A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.619A pdb=" N GLU C1143 " --> pdb=" O ALA C1139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.744A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 3.523A pdb=" N ASP C1188 " --> pdb=" O PRO C1185 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1185 through 1189' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.841A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1262 through 1266 removed outlier: 3.786A pdb=" N PHE C1265 " --> pdb=" O LYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.587A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 4.058A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.862A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 4.169A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.636A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.698A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.770A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.047A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.836A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 264 through 286 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.902A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.511A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.928A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.786A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.540A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.944A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.658A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.501A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.887A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 929 removed outlier: 3.526A pdb=" N GLN D 929 " --> pdb=" O PRO D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 926 through 929' Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.658A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.758A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 4.341A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1289 removed outlier: 3.529A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 4.121A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.640A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1354 Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.042A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.819A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.525A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 90 removed outlier: 3.624A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 Processing helix chain 'F' and resid 21 through 39 removed outlier: 3.612A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.744A pdb=" N GLU F 74 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 80 removed outlier: 3.513A pdb=" N ALA F 79 " --> pdb=" O THR F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 113 through 131 removed outlier: 3.572A pdb=" N MET F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 207 through 211 removed outlier: 3.528A pdb=" N ARG F 210 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 287 Processing helix chain 'F' and resid 314 through 319 removed outlier: 3.704A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 removed outlier: 3.763A pdb=" N LEU F 327 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER F 329 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN F 330 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 364 removed outlier: 3.961A pdb=" N ILE F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 371 Processing helix chain 'F' and resid 399 through 404 Processing helix chain 'F' and resid 409 through 416 removed outlier: 3.792A pdb=" N ALA F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 420 Processing helix chain 'F' and resid 442 through 451 removed outlier: 3.724A pdb=" N ALA F 445 " --> pdb=" O ARG F 442 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE F 446 " --> pdb=" O ASP F 443 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA F 449 " --> pdb=" O PHE F 446 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA F 450 " --> pdb=" O LYS F 447 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG F 451 " --> pdb=" O LEU F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 462 removed outlier: 3.514A pdb=" N ALA F 460 " --> pdb=" O GLU F 457 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN F 462 " --> pdb=" O LEU F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 487 removed outlier: 3.886A pdb=" N ASN F 487 " --> pdb=" O MET F 483 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 19 removed outlier: 5.453A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 17 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.707A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 59 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.577A pdb=" N VAL A 110 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.701A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.701A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 56 removed outlier: 4.192A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 110 removed outlier: 4.224A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 133 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.620A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.300A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 96 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.747A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 159 removed outlier: 5.726A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE C 188 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 174 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 186 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 239 removed outlier: 4.037A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 231 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 333 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.771A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 260 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.167A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.957A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.675A pdb=" N MET C 653 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.558A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.889A pdb=" N ALA C 716 " --> pdb=" O ALA C 784 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 784 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 749 through 750 removed outlier: 7.061A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 1076 through 1080 removed outlier: 7.781A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 841 removed outlier: 5.823A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AC7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.696A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 467 " --> pdb=" O ASN D 424 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS D 469 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.696A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.598A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.804A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD3, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.638A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD5, first strand: chain 'D' and resid 552 through 556 removed outlier: 3.698A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD7, first strand: chain 'D' and resid 849 through 850 removed outlier: 4.083A pdb=" N ASP D 855 " --> pdb=" O LYS D 850 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.704A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE1, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AE2, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 4.075A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D1115 " --> pdb=" O GLY D1033 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.567A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1187 through 1189 Processing sheet with id=AE5, first strand: chain 'D' and resid 1278 through 1279 removed outlier: 5.174A pdb=" N ILE D1266 " --> pdb=" O SER D1303 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER D1303 " --> pdb=" O ILE D1266 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN D1268 " --> pdb=" O THR D1301 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 45 through 49 removed outlier: 3.619A pdb=" N THR F 58 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 138 through 141 Processing sheet with id=AE8, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.449A pdb=" N GLU F 159 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 221 through 222 removed outlier: 3.714A pdb=" N LYS F 239 " --> pdb=" O GLU F 222 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2781 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 13.45 Time building geometry restraints manager: 13.16 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: 9867 1.34 - 1.46: 5030 1.46 - 1.58: 14679 1.58 - 1.70: 132 1.70 - 1.82: 182 Bond restraints: 29890 Sorted by residual: bond pdb=" CA CYS B 176 " pdb=" CB CYS B 176 " ideal model delta sigma weight residual 1.526 1.559 -0.033 1.76e-02 3.23e+03 3.56e+00 bond pdb=" C3' DC T 3 " pdb=" O3' DC T 3 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" CB ASP B 197 " pdb=" CG ASP B 197 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.11e+00 bond pdb=" C GLU B 29 " pdb=" N PRO B 30 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C ALA F 11 " pdb=" N VAL F 12 " ideal model delta sigma weight residual 1.329 1.348 -0.019 1.40e-02 5.10e+03 1.76e+00 ... (remaining 29885 not shown) Histogram of bond angle deviations from ideal: 97.17 - 104.55: 669 104.55 - 111.92: 14425 111.92 - 119.30: 10597 119.30 - 126.67: 14698 126.67 - 134.05: 393 Bond angle restraints: 40782 Sorted by residual: angle pdb=" N VAL E 6 " pdb=" CA VAL E 6 " pdb=" C VAL E 6 " ideal model delta sigma weight residual 113.20 106.35 6.85 9.60e-01 1.09e+00 5.10e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 130.10 -8.40 1.80e+00 3.09e-01 2.18e+01 angle pdb=" N GLU C1012 " pdb=" CA GLU C1012 " pdb=" CB GLU C1012 " ideal model delta sigma weight residual 110.39 117.87 -7.48 1.66e+00 3.63e-01 2.03e+01 angle pdb=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 129.68 -7.98 1.80e+00 3.09e-01 1.97e+01 angle pdb=" C GLU E 42 " pdb=" N ASN E 43 " pdb=" CA ASN E 43 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.75e+01 ... (remaining 40777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.73: 17295 28.73 - 57.45: 765 57.45 - 86.18: 104 86.18 - 114.90: 5 114.90 - 143.63: 5 Dihedral angle restraints: 18174 sinusoidal: 7294 harmonic: 10880 Sorted by residual: dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta harmonic sigma weight residual -180.00 -118.49 -61.51 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA GLU B 29 " pdb=" C GLU B 29 " pdb=" N PRO B 30 " pdb=" CA PRO B 30 " ideal model delta harmonic sigma weight residual 180.00 -130.22 -49.78 0 5.00e+00 4.00e-02 9.91e+01 dihedral pdb=" O4' U R 4 " pdb=" C1' U R 4 " pdb=" N1 U R 4 " pdb=" C2 U R 4 " ideal model delta sinusoidal sigma weight residual 200.00 125.69 74.31 1 1.50e+01 4.44e-03 3.11e+01 ... (remaining 18171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3450 0.045 - 0.090: 993 0.090 - 0.135: 278 0.135 - 0.180: 28 0.180 - 0.225: 8 Chirality restraints: 4757 Sorted by residual: chirality pdb=" CB ILE C 850 " pdb=" CA ILE C 850 " pdb=" CG1 ILE C 850 " pdb=" CG2 ILE C 850 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE B 61 " pdb=" CA ILE B 61 " pdb=" CG1 ILE B 61 " pdb=" CG2 ILE B 61 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4754 not shown) Planarity restraints: 5164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " -0.063 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO B 30 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 57 " 0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO C 58 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO C 552 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " -0.040 5.00e-02 4.00e+02 ... (remaining 5161 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 362 2.63 - 3.20: 25750 3.20 - 3.76: 44725 3.76 - 4.33: 56894 4.33 - 4.90: 92151 Nonbonded interactions: 219882 Sorted by model distance: nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.060 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.070 2.170 nonbonded pdb=" N2 DG N 37 " pdb=" O2 DC T 3 " model vdw 2.136 2.496 nonbonded pdb=" O2 DC N 35 " pdb=" N2 DG T 5 " model vdw 2.168 2.496 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.198 2.440 ... (remaining 219877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.500 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 91.800 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.003 0.047 29890 Z= 0.189 Angle : 0.673 11.344 40782 Z= 0.357 Chirality : 0.046 0.225 4757 Planarity : 0.005 0.096 5164 Dihedral : 15.989 143.627 11156 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.04 % Allowed : 0.59 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.94 (0.13), residues: 3767 helix: -0.18 (0.15), residues: 1162 sheet: -1.28 (0.25), residues: 407 loop : -1.98 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1276 HIS 0.008 0.001 HIS D 113 PHE 0.024 0.001 PHE C 389 TYR 0.029 0.001 TYR B 177 ARG 0.008 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ILE cc_start: 0.7752 (mm) cc_final: 0.7507 (mm) REVERT: B 29 GLU cc_start: 0.7639 (tt0) cc_final: 0.7198 (mt-10) REVERT: B 127 GLN cc_start: 0.9302 (pm20) cc_final: 0.9013 (pm20) REVERT: C 47 TYR cc_start: 0.1638 (m-80) cc_final: -0.0655 (m-80) REVERT: C 187 GLU cc_start: 0.7845 (tp30) cc_final: 0.7336 (tt0) REVERT: C 337 PHE cc_start: 0.8611 (t80) cc_final: 0.8265 (t80) REVERT: C 488 MET cc_start: 0.8317 (mmm) cc_final: 0.7982 (mmm) REVERT: C 770 CYS cc_start: 0.8199 (t) cc_final: 0.7552 (t) REVERT: C 785 ASP cc_start: 0.7583 (m-30) cc_final: 0.6919 (m-30) REVERT: C 1023 HIS cc_start: 0.8881 (m90) cc_final: 0.8529 (m90) REVERT: C 1034 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8251 (ttp80) REVERT: C 1080 ASN cc_start: 0.8379 (m110) cc_final: 0.8077 (m-40) REVERT: D 466 MET cc_start: 0.7868 (mtt) cc_final: 0.7642 (mtt) REVERT: D 832 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8835 (mmmt) REVERT: E 46 THR cc_start: 0.9145 (p) cc_final: 0.8765 (t) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.4000 time to fit residues: 198.6693 Evaluate side-chains 223 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 7.9990 chunk 289 optimal weight: 30.0000 chunk 160 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 346 optimal weight: 50.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 365 GLN D 489 ASN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN D1244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 29890 Z= 0.571 Angle : 0.786 10.789 40782 Z= 0.406 Chirality : 0.048 0.224 4757 Planarity : 0.006 0.112 5164 Dihedral : 14.706 150.585 4879 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.76 % Favored : 91.19 % Rotamer: Outliers : 2.09 % Allowed : 11.20 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % Twisted General : 0.03 % 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: -1.98 (0.13), residues: 3767 helix: 0.06 (0.15), residues: 1199 sheet: -1.63 (0.25), residues: 403 loop : -2.15 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C1276 HIS 0.010 0.002 HIS D 113 PHE 0.028 0.003 PHE B 231 TYR 0.019 0.002 TYR A 177 ARG 0.024 0.001 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 224 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8065 (p90) REVERT: B 127 GLN cc_start: 0.9344 (pm20) cc_final: 0.9141 (pm20) REVERT: B 177 TYR cc_start: 0.7603 (p90) cc_final: 0.6849 (p90) REVERT: C 47 TYR cc_start: 0.2219 (m-80) cc_final: -0.0480 (m-80) REVERT: C 337 PHE cc_start: 0.8868 (t80) cc_final: 0.8304 (t80) REVERT: C 429 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8237 (mpp) REVERT: C 488 MET cc_start: 0.8371 (mmm) cc_final: 0.8133 (mmm) REVERT: C 1229 TYR cc_start: 0.8904 (m-80) cc_final: 0.8377 (m-80) REVERT: D 17 PHE cc_start: 0.8634 (p90) cc_final: 0.8043 (p90) REVERT: D 192 MET cc_start: 0.8795 (ptm) cc_final: 0.8543 (ppp) REVERT: D 1370 MET cc_start: 0.8613 (tpp) cc_final: 0.8147 (tmm) outliers start: 57 outliers final: 44 residues processed: 265 average time/residue: 0.3733 time to fit residues: 166.1656 Evaluate side-chains 255 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 288 optimal weight: 30.0000 chunk 236 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 347 optimal weight: 0.5980 chunk 375 optimal weight: 30.0000 chunk 309 optimal weight: 10.0000 chunk 344 optimal weight: 50.0000 chunk 118 optimal weight: 0.7980 chunk 278 optimal weight: 7.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN C1023 HIS D 80 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29890 Z= 0.215 Angle : 0.564 8.938 40782 Z= 0.294 Chirality : 0.043 0.213 4757 Planarity : 0.004 0.095 5164 Dihedral : 14.560 152.204 4879 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 2.23 % Allowed : 14.35 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.62 (0.14), residues: 3767 helix: 0.49 (0.16), residues: 1198 sheet: -1.36 (0.25), residues: 397 loop : -2.02 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C1276 HIS 0.006 0.001 HIS D 777 PHE 0.014 0.001 PHE C 57 TYR 0.016 0.001 TYR C1018 ARG 0.006 0.000 ARG C1034 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 3.512 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7293 (mt-10) REVERT: B 122 GLU cc_start: 0.7935 (mp0) cc_final: 0.7370 (mp0) REVERT: B 127 GLN cc_start: 0.9288 (pm20) cc_final: 0.9013 (pm20) REVERT: B 177 TYR cc_start: 0.7390 (p90) cc_final: 0.6393 (p90) REVERT: C 47 TYR cc_start: 0.1848 (m-80) cc_final: -0.0680 (m-80) REVERT: C 187 GLU cc_start: 0.7964 (tp30) cc_final: 0.7625 (tt0) REVERT: C 244 GLU cc_start: 0.8853 (pp20) cc_final: 0.8594 (pp20) REVERT: C 337 PHE cc_start: 0.8782 (t80) cc_final: 0.8251 (t80) REVERT: C 488 MET cc_start: 0.8379 (mmm) cc_final: 0.8112 (mmm) REVERT: C 685 MET cc_start: 0.7914 (tpp) cc_final: 0.7594 (tpp) REVERT: C 1164 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: C 1229 TYR cc_start: 0.8810 (m-80) cc_final: 0.8285 (m-80) REVERT: C 1273 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8440 (mtm) REVERT: D 17 PHE cc_start: 0.8497 (p90) cc_final: 0.8097 (p90) REVERT: D 192 MET cc_start: 0.8740 (ptm) cc_final: 0.8526 (ppp) REVERT: D 355 ILE cc_start: 0.8943 (mt) cc_final: 0.8627 (mt) REVERT: D 466 MET cc_start: 0.7742 (mtt) cc_final: 0.7229 (mtt) REVERT: D 495 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7844 (p0) REVERT: D 1370 MET cc_start: 0.8477 (tpp) cc_final: 0.8064 (tmm) outliers start: 61 outliers final: 41 residues processed: 265 average time/residue: 0.3820 time to fit residues: 170.1007 Evaluate side-chains 260 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 216 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 40.0000 chunk 261 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 348 optimal weight: 50.0000 chunk 369 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 330 optimal weight: 50.0000 chunk 99 optimal weight: 0.0670 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29890 Z= 0.206 Angle : 0.543 9.147 40782 Z= 0.282 Chirality : 0.042 0.219 4757 Planarity : 0.004 0.092 5164 Dihedral : 14.466 152.739 4879 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.11 % Favored : 92.86 % Rotamer: Outliers : 3.15 % Allowed : 16.00 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.41 (0.14), residues: 3767 helix: 0.75 (0.16), residues: 1193 sheet: -1.26 (0.26), residues: 391 loop : -1.93 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C1276 HIS 0.004 0.001 HIS C1023 PHE 0.014 0.001 PHE C 57 TYR 0.015 0.001 TYR C1018 ARG 0.014 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 232 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7903 (p90) REVERT: B 29 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7387 (mt-10) REVERT: B 122 GLU cc_start: 0.7964 (mp0) cc_final: 0.7411 (mp0) REVERT: B 177 TYR cc_start: 0.7557 (p90) cc_final: 0.6596 (p90) REVERT: C 47 TYR cc_start: 0.1859 (m-80) cc_final: -0.0610 (m-80) REVERT: C 337 PHE cc_start: 0.8794 (t80) cc_final: 0.8328 (t80) REVERT: C 488 MET cc_start: 0.8366 (mmm) cc_final: 0.8095 (mmm) REVERT: C 572 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8181 (mp) REVERT: C 685 MET cc_start: 0.7997 (tpp) cc_final: 0.7642 (tpp) REVERT: C 799 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8089 (p0) REVERT: C 952 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8202 (mp10) REVERT: C 1164 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6750 (m-10) REVERT: C 1229 TYR cc_start: 0.8794 (m-80) cc_final: 0.8215 (m-80) REVERT: C 1273 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8318 (mtm) REVERT: D 17 PHE cc_start: 0.8445 (p90) cc_final: 0.8160 (p90) REVERT: D 192 MET cc_start: 0.8673 (ptm) cc_final: 0.8457 (ppp) REVERT: D 355 ILE cc_start: 0.9055 (mt) cc_final: 0.8687 (mt) REVERT: D 466 MET cc_start: 0.7826 (mtt) cc_final: 0.7352 (mtt) REVERT: D 495 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7924 (p0) REVERT: D 523 GLU cc_start: 0.8245 (pp20) cc_final: 0.8029 (pp20) REVERT: D 551 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7061 (ptm-80) REVERT: D 1370 MET cc_start: 0.8480 (tpp) cc_final: 0.8044 (tmm) outliers start: 86 outliers final: 50 residues processed: 301 average time/residue: 0.3708 time to fit residues: 187.4269 Evaluate side-chains 272 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 214 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 274 optimal weight: 0.0980 chunk 152 optimal weight: 20.0000 chunk 315 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C1023 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29890 Z= 0.351 Angle : 0.621 9.073 40782 Z= 0.321 Chirality : 0.044 0.236 4757 Planarity : 0.005 0.093 5164 Dihedral : 14.496 153.941 4879 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.36 % Favored : 91.58 % Rotamer: Outliers : 3.77 % Allowed : 17.17 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.53 (0.14), residues: 3767 helix: 0.65 (0.16), residues: 1200 sheet: -1.38 (0.25), residues: 416 loop : -2.01 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1276 HIS 0.005 0.001 HIS D 364 PHE 0.017 0.002 PHE B 231 TYR 0.015 0.002 TYR C1018 ARG 0.004 0.000 ARG D 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 221 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8185 (p90) REVERT: B 29 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7444 (mt-10) REVERT: B 122 GLU cc_start: 0.8092 (mp0) cc_final: 0.7545 (mp0) REVERT: B 177 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.6892 (p90) REVERT: C 47 TYR cc_start: 0.2283 (m-80) cc_final: -0.0215 (m-80) REVERT: C 315 MET cc_start: 0.6814 (mmp) cc_final: 0.5959 (mmp) REVERT: C 337 PHE cc_start: 0.8864 (t80) cc_final: 0.8366 (t80) REVERT: C 429 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8514 (mpp) REVERT: C 447 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7990 (t70) REVERT: C 488 MET cc_start: 0.8422 (mmm) cc_final: 0.8125 (mmm) REVERT: C 572 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8193 (mp) REVERT: C 685 MET cc_start: 0.8059 (tpp) cc_final: 0.7698 (tpp) REVERT: C 714 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9109 (p) REVERT: C 1056 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8372 (m) REVERT: C 1164 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7047 (m-10) REVERT: C 1229 TYR cc_start: 0.8855 (m-80) cc_final: 0.8370 (m-80) REVERT: C 1273 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8471 (mtm) REVERT: D 17 PHE cc_start: 0.8554 (p90) cc_final: 0.8247 (p90) REVERT: D 192 MET cc_start: 0.8749 (ptm) cc_final: 0.8531 (ppp) REVERT: D 495 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7890 (p0) REVERT: D 551 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7019 (ptm-80) REVERT: D 1370 MET cc_start: 0.8589 (tpp) cc_final: 0.8038 (tmm) outliers start: 103 outliers final: 70 residues processed: 302 average time/residue: 0.3679 time to fit residues: 187.7002 Evaluate side-chains 293 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 212 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 0.7980 chunk 332 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 369 optimal weight: 0.0040 chunk 306 optimal weight: 1.9990 chunk 171 optimal weight: 0.0870 chunk 30 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 overall best weight: 0.9774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1268 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29890 Z= 0.167 Angle : 0.545 9.141 40782 Z= 0.280 Chirality : 0.042 0.248 4757 Planarity : 0.004 0.091 5164 Dihedral : 14.419 154.694 4879 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.89 % Allowed : 18.75 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.33 (0.14), residues: 3767 helix: 0.83 (0.16), residues: 1207 sheet: -1.11 (0.26), residues: 394 loop : -1.94 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C1276 HIS 0.028 0.001 HIS C1023 PHE 0.015 0.001 PHE D 377 TYR 0.016 0.001 TYR C1018 ARG 0.004 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 225 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7813 (p90) REVERT: B 29 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7269 (mt-10) REVERT: B 122 GLU cc_start: 0.8059 (mp0) cc_final: 0.7542 (mp0) REVERT: B 142 MET cc_start: 0.8885 (mmm) cc_final: 0.8505 (mmm) REVERT: B 177 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.6738 (p90) REVERT: C 47 TYR cc_start: 0.2037 (m-80) cc_final: -0.0342 (m-80) REVERT: C 315 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.5906 (mmp) REVERT: C 337 PHE cc_start: 0.8709 (t80) cc_final: 0.8188 (t80) REVERT: C 447 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7843 (t-170) REVERT: C 488 MET cc_start: 0.8479 (mmm) cc_final: 0.8193 (mmm) REVERT: C 572 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8100 (mp) REVERT: C 685 MET cc_start: 0.8027 (tpp) cc_final: 0.7640 (tpp) REVERT: C 952 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: C 1034 ARG cc_start: 0.8765 (tmm160) cc_final: 0.8559 (ttp80) REVERT: C 1164 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: C 1229 TYR cc_start: 0.8799 (m-80) cc_final: 0.8181 (m-80) REVERT: C 1273 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: D 17 PHE cc_start: 0.8536 (p90) cc_final: 0.8236 (p90) REVERT: D 466 MET cc_start: 0.7663 (mtt) cc_final: 0.7403 (mtt) REVERT: D 495 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7875 (p0) REVERT: D 551 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.6976 (ptm-80) REVERT: D 1370 MET cc_start: 0.8545 (tpp) cc_final: 0.8075 (tmm) outliers start: 79 outliers final: 53 residues processed: 286 average time/residue: 0.3705 time to fit residues: 178.5028 Evaluate side-chains 278 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 215 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 311 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 368 optimal weight: 40.0000 chunk 230 optimal weight: 3.9990 chunk 224 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C1023 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29890 Z= 0.346 Angle : 0.630 9.820 40782 Z= 0.321 Chirality : 0.044 0.256 4757 Planarity : 0.005 0.094 5164 Dihedral : 14.459 154.834 4879 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.68 % Favored : 91.27 % Rotamer: Outliers : 3.88 % Allowed : 18.89 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.43 (0.14), residues: 3767 helix: 0.77 (0.16), residues: 1208 sheet: -1.22 (0.26), residues: 401 loop : -2.01 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1276 HIS 0.005 0.001 HIS A 66 PHE 0.016 0.002 PHE B 231 TYR 0.014 0.002 TYR C1018 ARG 0.004 0.000 ARG D 634 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 222 time to evaluate : 3.336 Fit side-chains revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8245 (p90) REVERT: B 29 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7454 (mt-10) REVERT: B 122 GLU cc_start: 0.8152 (mp0) cc_final: 0.7607 (mp0) REVERT: B 142 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8650 (mmm) REVERT: B 172 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9089 (pp) REVERT: C 47 TYR cc_start: 0.2101 (m-80) cc_final: 0.0532 (m-80) REVERT: C 291 TYR cc_start: 0.8346 (t80) cc_final: 0.8080 (t80) REVERT: C 315 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.5922 (mmp) REVERT: C 337 PHE cc_start: 0.8793 (t80) cc_final: 0.8257 (t80) REVERT: C 429 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8504 (mpp) REVERT: C 447 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7969 (t-170) REVERT: C 488 MET cc_start: 0.8467 (mmm) cc_final: 0.8162 (mmm) REVERT: C 572 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 685 MET cc_start: 0.8046 (tpp) cc_final: 0.7708 (tpp) REVERT: C 1027 LYS cc_start: 0.9198 (ptmt) cc_final: 0.8831 (pttm) REVERT: C 1056 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8405 (m) REVERT: C 1164 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: C 1229 TYR cc_start: 0.8844 (m-80) cc_final: 0.8302 (m-80) REVERT: C 1232 MET cc_start: 0.8346 (ttm) cc_final: 0.8050 (ttm) REVERT: C 1268 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7939 (mm-40) REVERT: C 1273 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8432 (mtm) REVERT: D 17 PHE cc_start: 0.8653 (p90) cc_final: 0.8392 (p90) REVERT: D 466 MET cc_start: 0.7885 (mtt) cc_final: 0.7553 (mtt) REVERT: D 495 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7913 (p0) REVERT: D 551 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7076 (ptm-80) REVERT: D 897 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7494 (t-90) REVERT: D 960 LEU cc_start: 0.8588 (mm) cc_final: 0.8025 (tp) REVERT: D 1370 MET cc_start: 0.8608 (tpp) cc_final: 0.8059 (tmm) REVERT: E 72 GLN cc_start: 0.8832 (pp30) cc_final: 0.8572 (pp30) outliers start: 106 outliers final: 69 residues processed: 304 average time/residue: 0.3671 time to fit residues: 188.8094 Evaluate side-chains 298 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 216 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 0.8980 chunk 147 optimal weight: 20.0000 chunk 219 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 250 optimal weight: 0.3980 chunk 182 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 289 optimal weight: 50.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS D 365 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29890 Z= 0.228 Angle : 0.566 9.080 40782 Z= 0.291 Chirality : 0.043 0.230 4757 Planarity : 0.004 0.091 5164 Dihedral : 14.421 155.602 4879 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.12 % Rotamer: Outliers : 3.48 % Allowed : 19.70 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.33 (0.14), residues: 3767 helix: 0.85 (0.16), residues: 1216 sheet: -1.11 (0.26), residues: 398 loop : -1.97 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C1276 HIS 0.004 0.001 HIS C1023 PHE 0.014 0.001 PHE C 57 TYR 0.014 0.001 TYR C1018 ARG 0.004 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 227 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8045 (p90) REVERT: B 29 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 122 GLU cc_start: 0.8127 (mp0) cc_final: 0.7556 (mp0) REVERT: C 47 TYR cc_start: 0.2060 (m-80) cc_final: 0.0514 (m-80) REVERT: C 291 TYR cc_start: 0.8324 (t80) cc_final: 0.8071 (t80) REVERT: C 315 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6094 (mmp) REVERT: C 337 PHE cc_start: 0.8768 (t80) cc_final: 0.8280 (t80) REVERT: C 429 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8536 (mpp) REVERT: C 447 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7922 (t-170) REVERT: C 488 MET cc_start: 0.8477 (mmm) cc_final: 0.8169 (mmm) REVERT: C 572 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8166 (mp) REVERT: C 1027 LYS cc_start: 0.9204 (ptmt) cc_final: 0.8838 (pttm) REVERT: C 1056 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8393 (m) REVERT: C 1164 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: C 1229 TYR cc_start: 0.8836 (m-80) cc_final: 0.8205 (m-80) REVERT: C 1268 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7902 (mm-40) REVERT: C 1273 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8290 (mtm) REVERT: D 17 PHE cc_start: 0.8613 (p90) cc_final: 0.8366 (p90) REVERT: D 466 MET cc_start: 0.7732 (mtt) cc_final: 0.7381 (mtt) REVERT: D 495 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7882 (p0) REVERT: D 551 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7047 (ptm-80) REVERT: D 897 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7419 (t-90) REVERT: D 960 LEU cc_start: 0.8739 (mm) cc_final: 0.8258 (tp) REVERT: D 1370 MET cc_start: 0.8563 (tpp) cc_final: 0.8031 (tmm) outliers start: 95 outliers final: 72 residues processed: 301 average time/residue: 0.3771 time to fit residues: 190.4000 Evaluate side-chains 301 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 218 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 6.9990 chunk 352 optimal weight: 40.0000 chunk 321 optimal weight: 0.7980 chunk 343 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 341 optimal weight: 50.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1288 GLN D 365 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 29890 Z= 0.508 Angle : 0.749 11.323 40782 Z= 0.380 Chirality : 0.047 0.269 4757 Planarity : 0.005 0.099 5164 Dihedral : 14.577 155.745 4879 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.93 % Favored : 90.02 % Rotamer: Outliers : 3.88 % Allowed : 19.63 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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 (0.14), residues: 3767 helix: 0.56 (0.16), residues: 1200 sheet: -1.55 (0.25), residues: 412 loop : -2.13 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C1276 HIS 0.008 0.002 HIS A 66 PHE 0.022 0.002 PHE B 231 TYR 0.016 0.002 TYR D 772 ARG 0.010 0.001 ARG D1148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 220 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8390 (p90) REVERT: B 122 GLU cc_start: 0.8244 (mp0) cc_final: 0.7582 (mp0) REVERT: B 172 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9092 (pp) REVERT: B 177 TYR cc_start: 0.7870 (p90) cc_final: 0.6978 (p90) REVERT: C 47 TYR cc_start: 0.2521 (m-80) cc_final: 0.0654 (m-80) REVERT: C 121 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: C 291 TYR cc_start: 0.8319 (t80) cc_final: 0.8042 (t80) REVERT: C 315 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6038 (mmp) REVERT: C 322 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8091 (mm) REVERT: C 337 PHE cc_start: 0.8902 (t80) cc_final: 0.8340 (t80) REVERT: C 429 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8551 (mpp) REVERT: C 447 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.8057 (t70) REVERT: C 488 MET cc_start: 0.8502 (mmm) cc_final: 0.8220 (mmm) REVERT: C 572 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8296 (mp) REVERT: C 1027 LYS cc_start: 0.9227 (ptmt) cc_final: 0.8882 (pttm) REVERT: C 1034 ARG cc_start: 0.8864 (tmm160) cc_final: 0.8565 (ttp80) REVERT: C 1056 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8488 (m) REVERT: C 1066 MET cc_start: 0.8445 (mtm) cc_final: 0.8242 (mtp) REVERT: C 1164 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: C 1229 TYR cc_start: 0.8915 (m-80) cc_final: 0.8469 (m-80) REVERT: C 1232 MET cc_start: 0.8361 (ttm) cc_final: 0.8055 (ttm) REVERT: C 1268 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8087 (mm-40) REVERT: C 1273 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8575 (mtm) REVERT: C 1276 TRP cc_start: 0.8584 (m-10) cc_final: 0.8361 (m-10) REVERT: D 17 PHE cc_start: 0.8737 (p90) cc_final: 0.8480 (p90) REVERT: D 466 MET cc_start: 0.7965 (mtt) cc_final: 0.7599 (mtt) REVERT: D 513 MET cc_start: 0.8734 (ttp) cc_final: 0.8530 (ttp) REVERT: D 551 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7213 (ptm-80) REVERT: D 897 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7614 (t-90) REVERT: D 903 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8677 (mm) REVERT: D 960 LEU cc_start: 0.8711 (mm) cc_final: 0.8207 (tp) REVERT: D 1028 ILE cc_start: 0.8890 (mm) cc_final: 0.8567 (tp) REVERT: D 1370 MET cc_start: 0.8619 (tpp) cc_final: 0.8117 (tmm) REVERT: E 72 GLN cc_start: 0.8828 (pp30) cc_final: 0.8568 (pp30) outliers start: 106 outliers final: 81 residues processed: 305 average time/residue: 0.3900 time to fit residues: 200.2047 Evaluate side-chains 309 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 214 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 0.9990 chunk 362 optimal weight: 8.9990 chunk 221 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 380 optimal weight: 10.0000 chunk 350 optimal weight: 50.0000 chunk 303 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1244 HIS C1288 GLN C1313 HIS D 365 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS D1366 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29890 Z= 0.190 Angle : 0.578 10.833 40782 Z= 0.296 Chirality : 0.044 0.516 4757 Planarity : 0.004 0.091 5164 Dihedral : 14.512 156.477 4879 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.42 % Rotamer: Outliers : 3.00 % Allowed : 20.80 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.34 (0.14), residues: 3767 helix: 0.88 (0.16), residues: 1202 sheet: -1.16 (0.26), residues: 394 loop : -1.97 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C1276 HIS 0.004 0.001 HIS C 165 PHE 0.016 0.001 PHE C 57 TYR 0.014 0.001 TYR C1018 ARG 0.012 0.000 ARG A 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 230 time to evaluate : 3.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8054 (p90) REVERT: B 29 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7355 (mt-10) REVERT: B 122 GLU cc_start: 0.8133 (mp0) cc_final: 0.7577 (mp0) REVERT: B 172 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9057 (pp) REVERT: C 47 TYR cc_start: 0.1855 (m-80) cc_final: 0.0129 (m-80) REVERT: C 247 ARG cc_start: 0.8883 (ptp-110) cc_final: 0.8553 (ptp-170) REVERT: C 315 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6104 (mmp) REVERT: C 337 PHE cc_start: 0.8829 (t80) cc_final: 0.8342 (t80) REVERT: C 429 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8514 (mpp) REVERT: C 447 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7899 (t-170) REVERT: C 488 MET cc_start: 0.8512 (mmm) cc_final: 0.8264 (mmm) REVERT: C 1023 HIS cc_start: 0.8914 (OUTLIER) cc_final: 0.8043 (t-170) REVERT: C 1027 LYS cc_start: 0.9215 (ptmt) cc_final: 0.8943 (ptpp) REVERT: C 1034 ARG cc_start: 0.8804 (tmm160) cc_final: 0.8486 (ttp80) REVERT: C 1056 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8418 (m) REVERT: C 1066 MET cc_start: 0.8449 (mtm) cc_final: 0.8225 (mtp) REVERT: C 1229 TYR cc_start: 0.8830 (m-80) cc_final: 0.8217 (m-80) REVERT: C 1268 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7958 (mm-40) REVERT: C 1273 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8199 (mtm) REVERT: D 17 PHE cc_start: 0.8616 (p90) cc_final: 0.8405 (p90) REVERT: D 75 TYR cc_start: 0.8205 (m-10) cc_final: 0.7933 (m-80) REVERT: D 466 MET cc_start: 0.7667 (mtt) cc_final: 0.7370 (mtt) REVERT: D 551 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7123 (ptm-80) REVERT: D 960 LEU cc_start: 0.8713 (mm) cc_final: 0.8223 (tp) REVERT: D 1028 ILE cc_start: 0.8896 (mm) cc_final: 0.8550 (tp) REVERT: D 1370 MET cc_start: 0.8510 (tpp) cc_final: 0.8074 (tmm) outliers start: 82 outliers final: 69 residues processed: 296 average time/residue: 0.3752 time to fit residues: 185.5834 Evaluate side-chains 300 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 222 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 893 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 5.9990 chunk 322 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 44 optimal weight: 50.0000 chunk 84 optimal weight: 10.0000 chunk 303 optimal weight: 0.0570 chunk 127 optimal weight: 0.6980 chunk 311 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1023 HIS ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.139392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087399 restraints weight = 58545.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090493 restraints weight = 29161.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.092606 restraints weight = 18716.974| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29890 Z= 0.168 Angle : 0.562 11.835 40782 Z= 0.287 Chirality : 0.043 0.476 4757 Planarity : 0.005 0.176 5164 Dihedral : 14.455 155.777 4879 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.93 % Allowed : 20.80 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 1.34 % 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: -1.21 (0.14), residues: 3767 helix: 0.98 (0.16), residues: 1210 sheet: -1.02 (0.26), residues: 399 loop : -1.91 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C1276 HIS 0.030 0.001 HIS C1023 PHE 0.014 0.001 PHE C 57 TYR 0.049 0.001 TYR D1365 ARG 0.014 0.000 ARG D1123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.76 seconds wall clock time: 95 minutes 46.24 seconds (5746.24 seconds total)