Starting phenix.real_space_refine on Tue Jul 7 01:10:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n81_49108/07_2026/9n81_49108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n81_49108/07_2026/9n81_49108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n81_49108/07_2026/9n81_49108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n81_49108/07_2026/9n81_49108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n81_49108/07_2026/9n81_49108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n81_49108/07_2026/9n81_49108.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 sd= 1.500 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 153 5.49 5 Mg 1 5.21 5 S 209 5.16 5 C 26173 2.51 5 N 7185 2.21 5 O 8167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41888 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4169 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 28, 'TRANS': 487} Chain breaks: 1 Chain: "B" Number of atoms: 4115 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 4104 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 512, 4104 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 bond proxies already assigned to first conformer: 4173 Chain: "C" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1887 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 12, 'TRANS': 225} Chain breaks: 1 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1633 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "F" Number of atoms: 5503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5503 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 25, 'TRANS': 653} Chain breaks: 3 Chain: "G" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "H" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "I" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "J" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 857 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "K" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 702 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 763 Classifications: {'DNA': 37} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 36} Chain: "M" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3389 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 27, 'TRANS': 400} Chain breaks: 3 Chain: "a" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4094 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 28, 'TRANS': 478} Chain: "b" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4100 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 23, 'TRANS': 487} Chain breaks: 1 Chain: "c" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1869 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 1 Chain: "d" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1623 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 3, 'TRANS': 196} Chain: "e" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1623 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 3, 'TRANS': 196} Chain: "f" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2069 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 10, 'TRANS': 244} Chain: "m" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 732 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DZ4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 315 " occ=0.55 ... (20 atoms not shown) pdb=" NH2BARG B 315 " occ=0.45 Time building chain proxies: 7.95, per 1000 atoms: 0.19 Number of scatterers: 41888 At special positions: 0 Unit cell: (209.916, 244.902, 191.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 209 16.00 P 153 15.00 Mg 1 11.99 O 8167 8.00 N 7185 7.00 C 26173 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 - 3.00 Amino acid : True - 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: 3.55 Conformation dependent library (CDL) restraints added in 1.7 seconds 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9202 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 43 sheets defined 46.4% alpha, 17.5% beta 73 base pairs and 124 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.685A pdb=" N TYR A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 58 through 78 removed outlier: 3.655A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.722A pdb=" N GLN A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.527A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 197 removed outlier: 3.940A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.249A pdb=" N GLU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.772A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.686A pdb=" N LYS A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 22 removed outlier: 4.163A pdb=" N SER B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.783A pdb=" N GLN B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 97 removed outlier: 3.545A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.698A pdb=" N ASP B 222 " --> pdb=" O ASP B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.901A pdb=" N LYS B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 482 " --> pdb=" O THR B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 482' Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.624A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.608A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.909A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing helix chain 'C' and resid 0 through 11 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.653A pdb=" N SER C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 86 Proline residue: C 82 - end of helix Processing helix chain 'C' and resid 127 through 170 removed outlier: 5.484A pdb=" N ARG C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.615A pdb=" N LEU C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 180 " --> pdb=" O ASP C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 180' Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.575A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 229 removed outlier: 3.541A pdb=" N TYR C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 299 removed outlier: 4.095A pdb=" N PHE C 298 " --> pdb=" O ARG C 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 60 removed outlier: 3.516A pdb=" N MET D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 Processing helix chain 'D' and resid 118 through 202 removed outlier: 3.944A pdb=" N VAL D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 30 Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 62 through 75 removed outlier: 3.753A pdb=" N VAL E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY E 68 " --> pdb=" O GLY E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 201 removed outlier: 3.705A pdb=" N GLY E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU E 170 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 182 " --> pdb=" O LYS E 178 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 15 through 29 removed outlier: 3.812A pdb=" N LEU F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 54 removed outlier: 3.614A pdb=" N LYS F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.939A pdb=" N LEU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 76 Processing helix chain 'F' and resid 85 through 98 Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 164 through 177 Processing helix chain 'F' and resid 179 through 192 Processing helix chain 'F' and resid 199 through 208 Processing helix chain 'F' and resid 211 through 218 Processing helix chain 'F' and resid 220 through 228 removed outlier: 3.861A pdb=" N VAL F 224 " --> pdb=" O ASP F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.688A pdb=" N ILE F 238 " --> pdb=" O GLY F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 263 removed outlier: 3.527A pdb=" N HIS F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU F 260 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET F 263 " --> pdb=" O GLU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 303 removed outlier: 4.036A pdb=" N PHE F 302 " --> pdb=" O TYR F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 381 through 390 removed outlier: 4.005A pdb=" N SER F 390 " --> pdb=" O TYR F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 424 Processing helix chain 'F' and resid 674 through 684 removed outlier: 3.607A pdb=" N ASN F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 715 Processing helix chain 'F' and resid 722 through 733 removed outlier: 4.353A pdb=" N LEU F 726 " --> pdb=" O LYS F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 755 Processing helix chain 'F' and resid 770 through 781 Processing helix chain 'F' and resid 788 through 804 Processing helix chain 'F' and resid 836 through 848 removed outlier: 4.053A pdb=" N ILE F 840 " --> pdb=" O THR F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 882 Processing helix chain 'F' and resid 891 through 901 removed outlier: 4.198A pdb=" N ASP F 899 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS F 900 " --> pdb=" O ASP F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 906 through 910 removed outlier: 3.627A pdb=" N LEU F 910 " --> pdb=" O ASN F 907 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 40 removed outlier: 4.091A pdb=" N MET M 39 " --> pdb=" O VAL M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 54 Processing helix chain 'M' and resid 75 through 88 Processing helix chain 'M' and resid 102 through 112 Processing helix chain 'M' and resid 153 through 171 Processing helix chain 'M' and resid 172 through 188 Processing helix chain 'M' and resid 195 through 200 removed outlier: 3.671A pdb=" N GLN M 200 " --> pdb=" O SER M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 220 Processing helix chain 'M' and resid 222 through 231 Processing helix chain 'M' and resid 231 through 242 Processing helix chain 'M' and resid 247 through 257 Processing helix chain 'M' and resid 261 through 267 removed outlier: 3.605A pdb=" N LEU M 265 " --> pdb=" O THR M 261 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG M 266 " --> pdb=" O LEU M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 282 Processing helix chain 'M' and resid 282 through 288 removed outlier: 3.645A pdb=" N THR M 288 " --> pdb=" O GLN M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 310 Processing helix chain 'M' and resid 319 through 324 removed outlier: 3.666A pdb=" N GLY M 324 " --> pdb=" O PHE M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 358 removed outlier: 3.836A pdb=" N ARG M 349 " --> pdb=" O GLY M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 436 removed outlier: 3.527A pdb=" N GLY M 436 " --> pdb=" O LEU M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 437 through 451 Processing helix chain 'M' and resid 474 through 482 removed outlier: 3.853A pdb=" N ILE M 478 " --> pdb=" O SER M 474 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE M 479 " --> pdb=" O GLU M 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'a' and resid 45 through 50 removed outlier: 3.778A pdb=" N GLU a 50 " --> pdb=" O ALA a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 78 Processing helix chain 'a' and resid 112 through 121 removed outlier: 3.681A pdb=" N GLN a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 135 Processing helix chain 'a' and resid 142 through 157 removed outlier: 3.826A pdb=" N VAL a 157 " --> pdb=" O LEU a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 180 through 197 Processing helix chain 'a' and resid 216 through 221 removed outlier: 4.194A pdb=" N ILE a 220 " --> pdb=" O PHE a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 244 removed outlier: 3.711A pdb=" N ASP a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 330 through 337 Processing helix chain 'a' and resid 357 through 361 removed outlier: 3.502A pdb=" N HIS a 360 " --> pdb=" O LYS a 357 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR a 361 " --> pdb=" O LYS a 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 357 through 361' Processing helix chain 'a' and resid 377 through 393 removed outlier: 3.632A pdb=" N LEU a 381 " --> pdb=" O GLY a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 439 through 443 removed outlier: 3.777A pdb=" N LYS a 443 " --> pdb=" O ALA a 440 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 469 Processing helix chain 'a' and resid 480 through 496 Processing helix chain 'a' and resid 510 through 519 Processing helix chain 'a' and resid 520 through 530 Processing helix chain 'b' and resid 17 through 21 Processing helix chain 'b' and resid 29 through 48 Processing helix chain 'b' and resid 87 through 96 removed outlier: 3.634A pdb=" N LEU b 91 " --> pdb=" O ASP b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 123 removed outlier: 3.601A pdb=" N ALA b 110 " --> pdb=" O ASP b 106 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 158 Processing helix chain 'b' and resid 198 through 216 Processing helix chain 'b' and resid 217 through 222 Processing helix chain 'b' and resid 227 through 234 Processing helix chain 'b' and resid 285 through 287 No H-bonds generated for 'chain 'b' and resid 285 through 287' Processing helix chain 'b' and resid 306 through 308 No H-bonds generated for 'chain 'b' and resid 306 through 308' Processing helix chain 'b' and resid 324 through 332 Processing helix chain 'b' and resid 352 through 356 Processing helix chain 'b' and resid 370 through 388 removed outlier: 3.512A pdb=" N ALA b 374 " --> pdb=" O ASP b 370 " (cutoff:3.500A) Processing helix chain 'b' and resid 447 through 461 Processing helix chain 'b' and resid 484 through 500 removed outlier: 3.577A pdb=" N GLN b 488 " --> pdb=" O ASN b 484 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 516 Processing helix chain 'b' and resid 519 through 526 removed outlier: 3.576A pdb=" N SER b 526 " --> pdb=" O VAL b 522 " (cutoff:3.500A) Processing helix chain 'b' and resid 526 through 537 Processing helix chain 'c' and resid 1 through 10 Processing helix chain 'c' and resid 51 through 62 removed outlier: 3.933A pdb=" N GLN c 56 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 68 through 86 Proline residue: c 82 - end of helix removed outlier: 3.595A pdb=" N ASP c 86 " --> pdb=" O PRO c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 135 Processing helix chain 'c' and resid 135 through 171 removed outlier: 3.683A pdb=" N GLY c 171 " --> pdb=" O TYR c 167 " (cutoff:3.500A) Processing helix chain 'c' and resid 185 through 197 Processing helix chain 'c' and resid 197 through 202 Processing helix chain 'c' and resid 207 through 214 Processing helix chain 'c' and resid 215 through 227 Processing helix chain 'd' and resid 49 through 60 Processing helix chain 'd' and resid 62 through 75 removed outlier: 3.509A pdb=" N TYR d 66 " --> pdb=" O GLU d 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL d 67 " --> pdb=" O LYS d 63 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY d 68 " --> pdb=" O GLY d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 200 removed outlier: 4.066A pdb=" N VAL d 122 " --> pdb=" O ASN d 118 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 60 Processing helix chain 'e' and resid 62 through 75 removed outlier: 3.583A pdb=" N TYR e 66 " --> pdb=" O GLU e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 199 removed outlier: 4.194A pdb=" N VAL e 122 " --> pdb=" O ASN e 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE e 123 " --> pdb=" O PRO e 119 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY e 160 " --> pdb=" O ASN e 156 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU e 170 " --> pdb=" O VAL e 166 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA e 171 " --> pdb=" O SER e 167 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU e 173 " --> pdb=" O LYS e 169 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR e 174 " --> pdb=" O GLU e 170 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU e 182 " --> pdb=" O LYS e 178 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL e 183 " --> pdb=" O ARG e 179 " (cutoff:3.500A) Processing helix chain 'f' and resid 674 through 685 removed outlier: 3.712A pdb=" N LEU f 678 " --> pdb=" O PRO f 674 " (cutoff:3.500A) Processing helix chain 'f' and resid 706 through 715 Processing helix chain 'f' and resid 722 through 733 removed outlier: 4.400A pdb=" N LEU f 726 " --> pdb=" O LYS f 722 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 743 removed outlier: 3.549A pdb=" N MET f 743 " --> pdb=" O PRO f 740 " (cutoff:3.500A) Processing helix chain 'f' and resid 747 through 758 removed outlier: 3.707A pdb=" N ARG f 756 " --> pdb=" O GLU f 752 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU f 757 " --> pdb=" O HIS f 753 " (cutoff:3.500A) Processing helix chain 'f' and resid 770 through 781 removed outlier: 3.556A pdb=" N ILE f 781 " --> pdb=" O VAL f 777 " (cutoff:3.500A) Processing helix chain 'f' and resid 788 through 803 removed outlier: 3.766A pdb=" N TYR f 803 " --> pdb=" O LEU f 799 " (cutoff:3.500A) Processing helix chain 'f' and resid 836 through 848 removed outlier: 3.708A pdb=" N ILE f 840 " --> pdb=" O THR f 836 " (cutoff:3.500A) Processing helix chain 'f' and resid 868 through 870 No H-bonds generated for 'chain 'f' and resid 868 through 870' Processing helix chain 'f' and resid 871 through 882 removed outlier: 3.730A pdb=" N ARG f 880 " --> pdb=" O LYS f 876 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR f 881 " --> pdb=" O ALA f 877 " (cutoff:3.500A) Processing helix chain 'f' and resid 890 through 901 removed outlier: 4.288A pdb=" N VAL f 894 " --> pdb=" O LYS f 890 " (cutoff:3.500A) Processing helix chain 'f' and resid 905 through 910 removed outlier: 3.501A pdb=" N GLN f 908 " --> pdb=" O GLU f 905 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU f 910 " --> pdb=" O ASN f 907 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 39 Processing helix chain 'm' and resid 40 through 54 Processing helix chain 'm' and resid 75 through 89 removed outlier: 3.711A pdb=" N ALA m 89 " --> pdb=" O ARG m 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 101 through 112 removed outlier: 3.822A pdb=" N LEU m 105 " --> pdb=" O ASP m 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 4.999A pdb=" N VAL A 104 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 87 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 108 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU A 83 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.764A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 431 " --> pdb=" O GLN A 416 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 349 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 304 removed outlier: 3.569A pdb=" N LYS A 297 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 296 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR B 295 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.651A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.323A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 247 through 253 removed outlier: 3.827A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU B 268 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N ASN B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 464 through 466 Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 17 removed outlier: 7.390A pdb=" N GLN C 48 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N HIS C 122 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N ASP C 50 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 12.350A pdb=" N ASN C 120 " --> pdb=" O ASP C 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.689A pdb=" N GLU D 2 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA D 42 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 89 removed outlier: 4.114A pdb=" N PHE D 97 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY D 109 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 89 removed outlier: 5.854A pdb=" N LYS E 99 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ARG E 107 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 250 through 253 removed outlier: 7.116A pdb=" N LEU F 250 " --> pdb=" O TRP F 447 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS F 449 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA F 252 " --> pdb=" O LYS F 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 287 through 292 removed outlier: 13.196A pdb=" N MET F 332 " --> pdb=" O LYS F 345 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LYS F 345 " --> pdb=" O MET F 332 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA F 334 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 287 through 292 removed outlier: 3.814A pdb=" N MET F 371 " --> pdb=" O ILE F 327 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP F 329 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL F 369 " --> pdb=" O ASP F 329 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N GLU F 331 " --> pdb=" O PHE F 367 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE F 367 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N MET F 333 " --> pdb=" O CYS F 365 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N CYS F 365 " --> pdb=" O MET F 333 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TYR F 335 " --> pdb=" O CYS F 363 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N CYS F 363 " --> pdb=" O TYR F 335 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR F 364 " --> pdb=" O GLU F 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 688 through 689 removed outlier: 6.948A pdb=" N GLU F 663 " --> pdb=" O CYS F 699 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE F 701 " --> pdb=" O GLU F 663 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS F 665 " --> pdb=" O ILE F 701 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL F 721 " --> pdb=" O TYR F 698 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL F 700 " --> pdb=" O VAL F 721 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 818 through 820 removed outlier: 6.689A pdb=" N TYR F 819 " --> pdb=" O ILE F 864 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL F 863 " --> pdb=" O LEU F 889 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'M' and resid 32 through 33 Processing sheet with id=AC5, first strand: chain 'M' and resid 314 through 318 removed outlier: 4.162A pdb=" N ASP M 332 " --> pdb=" O THR M 318 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL M 415 " --> pdb=" O PHE M 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 455 through 456 Processing sheet with id=AC7, first strand: chain 'a' and resid 102 through 109 removed outlier: 4.898A pdb=" N VAL a 104 " --> pdb=" O PHE a 87 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE a 87 " --> pdb=" O VAL a 104 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU a 108 " --> pdb=" O LEU a 83 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU a 83 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP a 36 " --> pdb=" O LEU a 82 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ALA a 84 " --> pdb=" O ASP a 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU a 38 " --> pdb=" O ALA a 84 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL a 86 " --> pdb=" O LEU a 38 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE a 40 " --> pdb=" O VAL a 86 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR a 88 " --> pdb=" O PHE a 40 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL a 42 " --> pdb=" O TYR a 88 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG a 35 " --> pdb=" O HIS a 163 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ARG a 165 " --> pdb=" O ARG a 35 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER a 37 " --> pdb=" O ARG a 165 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET a 167 " --> pdb=" O SER a 37 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE a 39 " --> pdb=" O MET a 167 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE a 169 " --> pdb=" O ILE a 39 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU a 41 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N PHE a 199 " --> pdb=" O SER a 162 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS a 164 " --> pdb=" O PHE a 199 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP a 201 " --> pdb=" O LYS a 164 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE a 166 " --> pdb=" O ASP a 201 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 257 through 262 removed outlier: 3.725A pdb=" N SER a 257 " --> pdb=" O ILE a 273 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL a 394 " --> pdb=" O PRO a 415 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG a 399 " --> pdb=" O LEU a 347 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU a 347 " --> pdb=" O ARG a 399 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR a 401 " --> pdb=" O LEU a 345 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU a 345 " --> pdb=" O THR a 401 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 286 through 289 removed outlier: 3.699A pdb=" N ASP b 319 " --> pdb=" O TYR b 316 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 296 through 304 removed outlier: 3.505A pdb=" N ARG a 301 " --> pdb=" O GLU b 292 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 326 through 329 Processing sheet with id=AD3, first strand: chain 'a' and resid 375 through 376 Processing sheet with id=AD4, first strand: chain 'a' and resid 419 through 420 removed outlier: 6.532A pdb=" N GLU a 419 " --> pdb=" O VAL a 427 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 77 through 84 removed outlier: 5.446A pdb=" N VAL b 79 " --> pdb=" O LEU b 58 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU b 58 " --> pdb=" O VAL b 79 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU b 83 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE b 54 " --> pdb=" O LEU b 83 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG b 130 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLN b 162 " --> pdb=" O ARG b 130 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE b 132 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE b 164 " --> pdb=" O ILE b 132 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE b 134 " --> pdb=" O PHE b 164 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N TYR b 225 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE b 163 " --> pdb=" O TYR b 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b' and resid 247 through 253 removed outlier: 3.908A pdb=" N LEU b 257 " --> pdb=" O ILE b 253 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL b 361 " --> pdb=" O SER b 266 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU b 268 " --> pdb=" O ASN b 359 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N ASN b 359 " --> pdb=" O LEU b 268 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N GLN b 360 " --> pdb=" O GLN b 423 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN b 423 " --> pdb=" O GLN b 360 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA b 366 " --> pdb=" O GLU b 417 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N GLU b 417 " --> pdb=" O ALA b 366 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N MET b 389 " --> pdb=" O PRO b 410 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG b 394 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL b 342 " --> pdb=" O ARG b 394 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ALA b 396 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE b 340 " --> pdb=" O ALA b 396 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE b 340 " --> pdb=" O PRO b 248 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ARG b 250 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL b 342 " --> pdb=" O ARG b 250 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR b 252 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLY b 344 " --> pdb=" O THR b 252 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 464 through 467 Processing sheet with id=AD8, first strand: chain 'c' and resid 14 through 18 removed outlier: 6.739A pdb=" N GLN c 48 " --> pdb=" O HIS c 122 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N HIS c 122 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N ASP c 50 " --> pdb=" O ASN c 120 " (cutoff:3.500A) removed outlier: 12.161A pdb=" N ASN c 120 " --> pdb=" O ASP c 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 65 through 66 removed outlier: 3.662A pdb=" N THR c 66 " --> pdb=" O SER e 105 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 2 through 9 Processing sheet with id=AE2, first strand: chain 'd' and resid 84 through 89 removed outlier: 3.575A pdb=" N PHE d 97 " --> pdb=" O GLY d 109 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY d 109 " --> pdb=" O PHE d 97 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS d 99 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG d 107 " --> pdb=" O LYS d 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'e' and resid 2 through 8 Processing sheet with id=AE4, first strand: chain 'e' and resid 83 through 89 removed outlier: 4.254A pdb=" N VAL e 83 " --> pdb=" O ASN e 100 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 688 through 690 removed outlier: 6.162A pdb=" N PHE f 664 " --> pdb=" O VAL f 690 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE f 701 " --> pdb=" O GLU f 663 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS f 665 " --> pdb=" O ILE f 701 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL f 700 " --> pdb=" O VAL f 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'f' and resid 851 through 852 removed outlier: 6.394A pdb=" N THR f 817 " --> pdb=" O HIS f 862 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE f 864 " --> pdb=" O THR f 817 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR f 819 " --> pdb=" O ILE f 864 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'm' and resid 32 through 34 removed outlier: 6.222A pdb=" N VAL m 69 " --> pdb=" O LEU m 100 " (cutoff:3.500A) 1960 hydrogen bonds defined for protein. 5593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 176 hydrogen bonds 352 hydrogen bond angles 0 basepair planarities 73 basepair parallelities 124 stacking parallelities Total time for adding SS restraints: 9.43 Time building geometry restraints manager: 4.53 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: 13009 1.34 - 1.46: 6801 1.46 - 1.58: 22606 1.58 - 1.70: 304 1.70 - 1.81: 329 Bond restraints: 43049 Sorted by residual: bond pdb=" O3B DZ4 M 502 " pdb=" PG DZ4 M 502 " ideal model delta sigma weight residual 1.745 1.604 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" O2A DZ4 M 502 " pdb=" PA DZ4 M 502 " ideal model delta sigma weight residual 1.502 1.607 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" O2B DZ4 M 502 " pdb=" PB DZ4 M 502 " ideal model delta sigma weight residual 1.532 1.604 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O5' DZ4 M 502 " pdb=" PA DZ4 M 502 " ideal model delta sigma weight residual 1.669 1.605 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C3' DA L 28 " pdb=" C2' DA L 28 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.54e+00 ... (remaining 43044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 58726 5.00 - 10.00: 17 10.00 - 15.01: 1 15.01 - 20.01: 0 20.01 - 25.01: 1 Bond angle restraints: 58745 Sorted by residual: angle pdb=" PA DZ4 M 502 " pdb=" N3A DZ4 M 502 " pdb=" PB DZ4 M 502 " ideal model delta sigma weight residual 135.12 110.11 25.01 3.00e+00 1.11e-01 6.95e+01 angle pdb=" N3 DT L 34 " pdb=" C4 DT L 34 " pdb=" O4 DT L 34 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 49 " pdb=" C4 DT I 49 " pdb=" O4 DT I 49 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT L 35 " pdb=" C4 DT L 35 " pdb=" O4 DT L 35 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT L 33 " pdb=" C4 DT L 33 " pdb=" O4 DT L 33 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 58740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 23087 25.68 - 51.36: 2403 51.36 - 77.03: 398 77.03 - 102.71: 40 102.71 - 128.39: 2 Dihedral angle restraints: 25930 sinusoidal: 11801 harmonic: 14129 Sorted by residual: dihedral pdb=" C5' DZ4 M 502 " pdb=" O5' DZ4 M 502 " pdb=" PA DZ4 M 502 " pdb=" N3A DZ4 M 502 " ideal model delta sinusoidal sigma weight residual 68.60 -163.01 -128.39 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C5' DZ4 M 502 " pdb=" O5' DZ4 M 502 " pdb=" PA DZ4 M 502 " pdb=" O2A DZ4 M 502 " ideal model delta sinusoidal sigma weight residual 180.42 76.66 103.76 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CA GLU c 196 " pdb=" C GLU c 196 " pdb=" N LYS c 197 " pdb=" CA LYS c 197 " ideal model delta harmonic sigma weight residual -180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 25927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5830 0.066 - 0.133: 574 0.133 - 0.199: 115 0.199 - 0.266: 1 0.266 - 0.332: 1 Chirality restraints: 6521 Sorted by residual: chirality pdb=" C4' DZ4 M 502 " pdb=" C3' DZ4 M 502 " pdb=" C5' DZ4 M 502 " pdb=" O4' DZ4 M 502 " both_signs ideal model delta sigma weight residual False -2.38 -2.72 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C3' DZ4 M 502 " pdb=" C2' DZ4 M 502 " pdb=" C4' DZ4 M 502 " pdb=" O3' DZ4 M 502 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C3' DG J 39 " pdb=" C4' DG J 39 " pdb=" O3' DG J 39 " pdb=" C2' DG J 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 6518 not shown) Planarity restraints: 7028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG e 179 " 0.251 9.50e-02 1.11e+02 1.13e-01 7.78e+00 pdb=" NE ARG e 179 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG e 179 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG e 179 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG e 179 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 161 " -0.147 9.50e-02 1.11e+02 6.62e-02 2.75e+00 pdb=" NE ARG E 161 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 161 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 161 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 161 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG a 247 " 0.136 9.50e-02 1.11e+02 6.13e-02 2.75e+00 pdb=" NE ARG a 247 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG a 247 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG a 247 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG a 247 " 0.001 2.00e-02 2.50e+03 ... (remaining 7025 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 9 2.43 - 3.05: 25797 3.05 - 3.67: 61403 3.67 - 4.28: 89777 4.28 - 4.90: 149748 Nonbonded interactions: 326734 Sorted by model distance: nonbonded pdb=" OD2 ASP M 332 " pdb="MG MG M 501 " model vdw 1.814 2.170 nonbonded pdb=" OD1 ASP M 330 " pdb="MG MG M 501 " model vdw 1.835 2.170 nonbonded pdb="MG MG M 501 " pdb=" O2A DZ4 M 502 " model vdw 1.836 2.170 nonbonded pdb=" OD1 ASP M 332 " pdb="MG MG M 501 " model vdw 2.011 2.170 nonbonded pdb=" CG ASP M 332 " pdb="MG MG M 501 " model vdw 2.162 2.400 ... (remaining 326729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 or resid 33 through 538)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 6 through 170 or resid 197 through 314 or resid 316 throug \ h 542)) selection = (chain 'b' and (resid 6 through 314 or resid 316 through 542)) } ncs_group { reference = (chain 'C' and (resid 0 through 227 or resid 293 through 299)) selection = chain 'c' } ncs_group { reference = (chain 'D' and resid 1 through 200) selection = (chain 'E' and resid 1 through 200) selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.730 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: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 38.670 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 0.141 43049 Z= 0.223 Angle : 0.518 25.011 58745 Z= 0.340 Chirality : 0.043 0.332 6521 Planarity : 0.004 0.113 7028 Dihedral : 19.296 128.389 16728 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.69 % Allowed : 21.87 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.13), residues: 4775 helix: 3.27 (0.12), residues: 1966 sheet: 0.69 (0.19), residues: 773 loop : -0.07 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 247 TYR 0.008 0.001 TYR C 34 PHE 0.011 0.001 PHE A 99 TRP 0.010 0.001 TRP m 82 HIS 0.002 0.000 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.22 (43049) covalent geometry : angle 0.51833 / 0.34 (58745) hydrogen bonds : bond 0.12687 / 8.09 ( 2122) hydrogen bonds : angle 4.92105 / 3.52 ( 5945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 711 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8093 (OUTLIER) cc_final: 0.7592 (p) REVERT: B 16 VAL cc_start: 0.9071 (m) cc_final: 0.8868 (t) REVERT: C 107 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7857 (mtt90) REVERT: D 84 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: D 112 ASN cc_start: 0.8006 (m-40) cc_final: 0.7325 (t0) REVERT: F 24 GLU cc_start: 0.7488 (tp30) cc_final: 0.7027 (tp30) REVERT: F 279 MET cc_start: 0.5092 (mtt) cc_final: 0.4493 (tpp) REVERT: F 371 MET cc_start: 0.7315 (ttt) cc_final: 0.6655 (mtt) REVERT: G 191 LYS cc_start: 0.9152 (pttt) cc_final: 0.8946 (ptmm) REVERT: M 25 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7721 (m) REVERT: M 33 TYR cc_start: 0.6505 (t80) cc_final: 0.6195 (t80) REVERT: a 53 SER cc_start: 0.6877 (OUTLIER) cc_final: 0.6520 (p) REVERT: a 135 MET cc_start: 0.8672 (mtt) cc_final: 0.8313 (mtt) REVERT: a 409 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: b 434 MET cc_start: 0.8571 (mmp) cc_final: 0.8304 (tmt) REVERT: c 105 ILE cc_start: 0.8541 (mm) cc_final: 0.8327 (mm) REVERT: d 70 LEU cc_start: 0.9441 (mt) cc_final: 0.9212 (mp) REVERT: e 59 MET cc_start: 0.4872 (mmt) cc_final: 0.4651 (mpp) REVERT: e 82 ASP cc_start: 0.7209 (m-30) cc_final: 0.7003 (m-30) REVERT: f 743 MET cc_start: 0.7319 (ttm) cc_final: 0.7102 (ttp) REVERT: m 35 VAL cc_start: 0.8780 (m) cc_final: 0.7960 (m) REVERT: m 39 MET cc_start: 0.8136 (ptp) cc_final: 0.7442 (ptm) REVERT: m 68 HIS cc_start: 0.6029 (m90) cc_final: 0.5798 (m90) outliers start: 73 outliers final: 20 residues processed: 761 average time/residue: 0.7670 time to fit residues: 705.4998 Evaluate side-chains 443 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 417 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 68 HIS Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain m residue 95 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 0.0370 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 4.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 293 ASN A 405 ASN B 45 GLN B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 517 ASN C 48 GLN D 143 HIS F 27 GLN F 200 GLN F 227 GLN a 65 GLN b 80 HIS c 17 GLN c 133 GLN ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 121 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.106464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070853 restraints weight = 175908.478| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 4.59 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 43049 Z= 0.174 Angle : 0.609 9.042 58745 Z= 0.327 Chirality : 0.041 0.162 6521 Planarity : 0.004 0.081 7028 Dihedral : 15.936 115.334 6929 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.20 % Allowed : 24.77 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.13), residues: 4775 helix: 2.89 (0.12), residues: 1987 sheet: 0.59 (0.19), residues: 758 loop : -0.12 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 71 TYR 0.020 0.001 TYR B 416 PHE 0.026 0.001 PHE B 107 TRP 0.029 0.001 TRP f 805 HIS 0.007 0.001 HIS F 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (43049) covalent geometry : angle 0.60910 / 0.33 (58745) hydrogen bonds : bond 0.04568 / 3.00 ( 2122) hydrogen bonds : angle 4.30106 / 3.09 ( 5945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 431 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8947 (tpp) cc_final: 0.8733 (tmm) REVERT: A 422 ASP cc_start: 0.8360 (p0) cc_final: 0.7597 (p0) REVERT: B 103 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: B 107 PHE cc_start: 0.9103 (p90) cc_final: 0.8484 (p90) REVERT: B 292 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: B 319 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: D 84 TYR cc_start: 0.8345 (m-80) cc_final: 0.7894 (m-80) REVERT: D 112 ASN cc_start: 0.9064 (m-40) cc_final: 0.8277 (t0) REVERT: D 145 GLN cc_start: 0.9467 (tp40) cc_final: 0.9266 (mm110) REVERT: D 157 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8536 (p0) REVERT: E 180 PHE cc_start: 0.7615 (m-80) cc_final: 0.7232 (m-80) REVERT: F 61 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8932 (t) REVERT: F 68 MET cc_start: 0.8925 (tpp) cc_final: 0.8650 (tpp) REVERT: F 371 MET cc_start: 0.8176 (ttt) cc_final: 0.7741 (mtt) REVERT: G 191 LYS cc_start: 0.9155 (pttt) cc_final: 0.8933 (ptmm) REVERT: M 255 TYR cc_start: 0.9092 (t80) cc_final: 0.8820 (t80) REVERT: a 312 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8832 (tt) REVERT: a 409 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: b 434 MET cc_start: 0.8255 (mmp) cc_final: 0.7887 (tmt) REVERT: c 63 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8019 (mmpt) REVERT: c 109 ARG cc_start: 0.7566 (ttt180) cc_final: 0.7044 (tmt170) REVERT: c 176 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6259 (ptp-170) REVERT: d 24 TRP cc_start: 0.8684 (p90) cc_final: 0.8464 (p90) REVERT: d 70 LEU cc_start: 0.9547 (mt) cc_final: 0.9282 (mp) REVERT: d 194 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8510 (tm) REVERT: e 55 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8953 (tm-30) REVERT: e 71 ARG cc_start: 0.8999 (ptp-110) cc_final: 0.8795 (ptp-110) REVERT: e 82 ASP cc_start: 0.7827 (m-30) cc_final: 0.7342 (m-30) REVERT: f 743 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7833 (ttp) REVERT: f 812 MET cc_start: 0.8540 (tmt) cc_final: 0.8275 (ppp) REVERT: f 819 TYR cc_start: 0.5879 (t80) cc_final: 0.5573 (t80) REVERT: m 33 TYR cc_start: 0.7607 (t80) cc_final: 0.7335 (t80) REVERT: m 35 VAL cc_start: 0.7719 (m) cc_final: 0.7406 (m) REVERT: m 94 CYS cc_start: 0.0395 (OUTLIER) cc_final: -0.0281 (m) REVERT: m 105 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9217 (tm) outliers start: 138 outliers final: 44 residues processed: 530 average time/residue: 0.7784 time to fit residues: 502.6383 Evaluate side-chains 435 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 377 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 264 ASP Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 63 LYS Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 176 ARG Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 194 LEU Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 175 ASP Chi-restraints excluded: chain f residue 743 MET Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 94 CYS Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 101 ASP Chi-restraints excluded: chain m residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 321 optimal weight: 2.9990 chunk 483 optimal weight: 6.9990 chunk 452 optimal weight: 0.6980 chunk 306 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 309 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 284 optimal weight: 4.9990 chunk 283 optimal weight: 0.5980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 360 HIS A 423 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN F 258 HIS F 816 HIS M 68 HIS a 68 GLN d 87 ASN ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 185 ASN f 745 HIS ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS ** f 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.105115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.070659 restraints weight = 153880.429| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 4.46 r_work: 0.3053 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 43049 Z= 0.194 Angle : 0.592 9.845 58745 Z= 0.313 Chirality : 0.040 0.172 6521 Planarity : 0.004 0.061 7028 Dihedral : 16.274 112.899 6907 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.25 % Allowed : 24.14 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.12), residues: 4775 helix: 2.68 (0.12), residues: 1973 sheet: 0.59 (0.18), residues: 746 loop : -0.20 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 71 TYR 0.025 0.002 TYR c 167 PHE 0.022 0.001 PHE B 107 TRP 0.046 0.001 TRP f 805 HIS 0.015 0.001 HIS M 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (43049) covalent geometry : angle 0.59209 / 0.31 (58745) hydrogen bonds : bond 0.04367 / 2.88 ( 2122) hydrogen bonds : angle 4.23120 / 3.04 ( 5945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 399 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8072 (tpp) REVERT: A 312 LEU cc_start: 0.8728 (mm) cc_final: 0.8396 (tt) REVERT: C 23 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8732 (pp) REVERT: C 47 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: C 152 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: C 165 GLN cc_start: 0.9073 (tt0) cc_final: 0.8862 (tm-30) REVERT: D 112 ASN cc_start: 0.9109 (m-40) cc_final: 0.8317 (t0) REVERT: D 145 GLN cc_start: 0.9573 (tp40) cc_final: 0.9341 (mm110) REVERT: D 157 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8584 (p0) REVERT: E 157 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8714 (p0) REVERT: E 180 PHE cc_start: 0.7960 (m-80) cc_final: 0.7523 (m-80) REVERT: F 61 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9043 (t) REVERT: F 263 MET cc_start: -0.1365 (ptp) cc_final: -0.1647 (ptp) REVERT: F 371 MET cc_start: 0.7964 (ttt) cc_final: 0.7298 (mtt) REVERT: F 783 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7683 (t0) REVERT: G 191 LYS cc_start: 0.9160 (pttt) cc_final: 0.8896 (ptmm) REVERT: H 183 GLU cc_start: 0.8462 (tp30) cc_final: 0.8228 (tp30) REVERT: H 191 LYS cc_start: 0.8886 (tppt) cc_final: 0.8568 (tppt) REVERT: M 33 TYR cc_start: 0.6902 (t80) cc_final: 0.6635 (t80) REVERT: M 138 MET cc_start: 0.8804 (tpp) cc_final: 0.8306 (tpt) REVERT: M 255 TYR cc_start: 0.9160 (t80) cc_final: 0.8866 (t80) REVERT: M 394 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8956 (tm) REVERT: a 134 MET cc_start: 0.9245 (tmm) cc_final: 0.8952 (tmm) REVERT: a 312 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8845 (tt) REVERT: a 404 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8563 (mtm-85) REVERT: a 409 TYR cc_start: 0.9241 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: a 514 MET cc_start: 0.8856 (mtm) cc_final: 0.8554 (mtp) REVERT: b 434 MET cc_start: 0.8921 (mmp) cc_final: 0.8138 (tmt) REVERT: c 63 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7813 (mmpt) REVERT: c 194 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9105 (mpp) REVERT: d 24 TRP cc_start: 0.8775 (p90) cc_final: 0.8507 (p90) REVERT: d 72 LYS cc_start: 0.9431 (ttpt) cc_final: 0.9052 (ptmm) REVERT: e 55 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8878 (tm-30) REVERT: e 59 MET cc_start: 0.5559 (mmt) cc_final: 0.5230 (mmt) REVERT: e 82 ASP cc_start: 0.7793 (m-30) cc_final: 0.7353 (m-30) REVERT: f 746 MET cc_start: 0.8883 (mpp) cc_final: 0.8329 (mmt) REVERT: f 805 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7512 (m100) REVERT: f 812 MET cc_start: 0.8513 (tmm) cc_final: 0.8208 (tmt) REVERT: f 819 TYR cc_start: 0.6830 (t80) cc_final: 0.6273 (t80) REVERT: m 33 TYR cc_start: 0.7755 (t80) cc_final: 0.7406 (t80) REVERT: m 35 VAL cc_start: 0.7474 (m) cc_final: 0.7062 (m) REVERT: m 71 MET cc_start: 0.8131 (tpp) cc_final: 0.7921 (tpp) REVERT: m 94 CYS cc_start: 0.0174 (OUTLIER) cc_final: -0.0623 (m) REVERT: m 101 ASP cc_start: 0.9005 (t70) cc_final: 0.8720 (t70) REVERT: m 105 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9180 (tm) outliers start: 140 outliers final: 57 residues processed: 503 average time/residue: 0.7775 time to fit residues: 479.2579 Evaluate side-chains 439 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 364 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 249 LYS Chi-restraints excluded: chain M residue 264 ASP Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain M residue 394 LEU Chi-restraints excluded: chain a residue 139 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 281 LEU Chi-restraints excluded: chain a residue 298 THR Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 404 ARG Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 62 ASN Chi-restraints excluded: chain c residue 63 LYS Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 194 MET Chi-restraints excluded: chain c residue 226 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 183 VAL Chi-restraints excluded: chain f residue 764 SER Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 805 TRP Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 94 CYS Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 128 optimal weight: 6.9990 chunk 392 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 297 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN B 76 ASN B 103 GLN C 48 GLN C 147 GLN F 258 HIS ** F 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 HIS c 78 ASN c 122 HIS d 9 HIS ** d 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 87 ASN ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 185 ASN ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS ** f 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.102790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066947 restraints weight = 154744.736| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.24 r_work: 0.3001 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 43049 Z= 0.286 Angle : 0.646 11.890 58745 Z= 0.338 Chirality : 0.042 0.165 6521 Planarity : 0.005 0.061 7028 Dihedral : 16.723 112.482 6906 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.90 % Allowed : 24.00 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.12), residues: 4775 helix: 2.42 (0.12), residues: 1976 sheet: 0.40 (0.18), residues: 766 loop : -0.30 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 681 TYR 0.027 0.002 TYR d 129 PHE 0.028 0.002 PHE B 107 TRP 0.034 0.002 TRP f 805 HIS 0.012 0.001 HIS M 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.29 (43049) covalent geometry : angle 0.64643 / 0.34 (58745) hydrogen bonds : bond 0.04791 / 3.17 ( 2122) hydrogen bonds : angle 4.34636 / 3.11 ( 5945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 387 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 LEU cc_start: 0.8767 (mm) cc_final: 0.8416 (tt) REVERT: B 103 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: B 107 PHE cc_start: 0.8999 (p90) cc_final: 0.8299 (p90) REVERT: C 23 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8855 (pp) REVERT: C 47 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: C 165 GLN cc_start: 0.9093 (tt0) cc_final: 0.8878 (tm-30) REVERT: C 183 PRO cc_start: 0.9035 (Cg_exo) cc_final: 0.8786 (Cg_endo) REVERT: D 21 GLN cc_start: 0.9005 (tt0) cc_final: 0.8595 (tm130) REVERT: D 71 ARG cc_start: 0.9262 (ttm170) cc_final: 0.8860 (ttm110) REVERT: D 112 ASN cc_start: 0.9127 (m-40) cc_final: 0.8226 (t0) REVERT: D 157 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8661 (p0) REVERT: E 157 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8666 (p0) REVERT: E 180 PHE cc_start: 0.8225 (m-80) cc_final: 0.7633 (m-80) REVERT: F 61 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8988 (t) REVERT: F 263 MET cc_start: 0.6683 (ptp) cc_final: 0.6424 (ptp) REVERT: F 371 MET cc_start: 0.8210 (ttt) cc_final: 0.7685 (mtt) REVERT: F 743 MET cc_start: 0.9023 (mmt) cc_final: 0.8595 (mmt) REVERT: F 783 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7781 (t0) REVERT: G 191 LYS cc_start: 0.9170 (pttt) cc_final: 0.8895 (ptmm) REVERT: H 183 GLU cc_start: 0.8520 (tp30) cc_final: 0.8290 (tp30) REVERT: H 191 LYS cc_start: 0.8853 (tppt) cc_final: 0.8376 (tppt) REVERT: M 33 TYR cc_start: 0.7048 (t80) cc_final: 0.6840 (t80) REVERT: M 255 TYR cc_start: 0.9176 (t80) cc_final: 0.8870 (t80) REVERT: a 135 MET cc_start: 0.8782 (mmt) cc_final: 0.8546 (mmt) REVERT: a 312 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8855 (tt) REVERT: a 404 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8618 (mtm-85) REVERT: a 409 TYR cc_start: 0.9274 (OUTLIER) cc_final: 0.8625 (m-80) REVERT: b 434 MET cc_start: 0.8922 (mmp) cc_final: 0.8183 (tmt) REVERT: c 63 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7903 (mmpt) REVERT: c 80 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8942 (tm) REVERT: c 167 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7990 (t80) REVERT: e 55 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: e 59 MET cc_start: 0.5305 (mmt) cc_final: 0.4786 (mmm) REVERT: e 71 ARG cc_start: 0.9229 (ptp-110) cc_final: 0.8587 (ptp90) REVERT: e 82 ASP cc_start: 0.7850 (m-30) cc_final: 0.7367 (m-30) REVERT: e 185 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8253 (m110) REVERT: f 743 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8263 (ttp) REVERT: f 792 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8111 (mpp) REVERT: f 812 MET cc_start: 0.8598 (tmm) cc_final: 0.8308 (tmt) REVERT: f 819 TYR cc_start: 0.6963 (t80) cc_final: 0.6475 (t80) REVERT: m 94 CYS cc_start: -0.0060 (OUTLIER) cc_final: -0.0851 (m) REVERT: m 101 ASP cc_start: 0.9141 (t70) cc_final: 0.8849 (t70) outliers start: 168 outliers final: 69 residues processed: 518 average time/residue: 0.7430 time to fit residues: 472.3124 Evaluate side-chains 447 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 360 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain M residue 249 LYS Chi-restraints excluded: chain M residue 264 ASP Chi-restraints excluded: chain M residue 354 LEU Chi-restraints excluded: chain a residue 139 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 298 THR Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 404 ARG Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 475 SER Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 436 SER Chi-restraints excluded: chain b residue 515 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 63 LYS Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 226 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 185 ASN Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain f residue 682 ILE Chi-restraints excluded: chain f residue 743 MET Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 792 MET Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 94 CYS Chi-restraints excluded: chain m residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 158 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 60 optimal weight: 0.0020 chunk 122 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 149 optimal weight: 2.9990 overall best weight: 0.5908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN C 48 GLN F 258 HIS F 657 ASN c 62 ASN d 18 HIS d 87 ASN e 21 GLN e 185 ASN ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS ** f 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.104575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069160 restraints weight = 135772.231| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.30 r_work: 0.3066 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43049 Z= 0.130 Angle : 0.595 11.369 58745 Z= 0.309 Chirality : 0.040 0.258 6521 Planarity : 0.004 0.059 7028 Dihedral : 16.647 134.835 6903 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.90 % Allowed : 25.63 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.12), residues: 4775 helix: 2.57 (0.12), residues: 1969 sheet: 0.55 (0.18), residues: 756 loop : -0.25 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG d 71 TYR 0.025 0.001 TYR d 66 PHE 0.025 0.001 PHE B 107 TRP 0.028 0.001 TRP f 805 HIS 0.006 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (43049) covalent geometry : angle 0.59549 / 0.31 (58745) hydrogen bonds : bond 0.04043 / 2.66 ( 2122) hydrogen bonds : angle 4.13332 / 2.97 ( 5945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 384 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9051 (tpp) cc_final: 0.8687 (tpp) REVERT: A 265 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8736 (ptmm) REVERT: A 312 LEU cc_start: 0.8749 (mm) cc_final: 0.8413 (tt) REVERT: B 103 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: C 23 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8712 (pp) REVERT: C 47 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: C 152 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: C 165 GLN cc_start: 0.9073 (tt0) cc_final: 0.8627 (tp40) REVERT: C 180 LYS cc_start: 0.9376 (ttpp) cc_final: 0.9153 (tmmt) REVERT: D 112 ASN cc_start: 0.9117 (m-40) cc_final: 0.8390 (t0) REVERT: D 157 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8688 (p0) REVERT: E 157 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8691 (p0) REVERT: E 159 GLN cc_start: 0.8062 (mm110) cc_final: 0.7515 (mm-40) REVERT: E 165 CYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8579 (p) REVERT: F 61 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8999 (t) REVERT: F 263 MET cc_start: 0.7668 (ptp) cc_final: 0.7459 (ptp) REVERT: F 371 MET cc_start: 0.8152 (ttt) cc_final: 0.7646 (mtt) REVERT: F 783 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7749 (t0) REVERT: G 191 LYS cc_start: 0.9131 (pttt) cc_final: 0.8852 (ptmm) REVERT: H 191 LYS cc_start: 0.8883 (tppt) cc_final: 0.8398 (tppt) REVERT: M 138 MET cc_start: 0.8711 (tpp) cc_final: 0.8262 (tpt) REVERT: M 158 GLU cc_start: 0.8937 (tp30) cc_final: 0.8735 (tp30) REVERT: M 255 TYR cc_start: 0.9137 (t80) cc_final: 0.8853 (t80) REVERT: a 134 MET cc_start: 0.9254 (tmm) cc_final: 0.9014 (tmm) REVERT: a 135 MET cc_start: 0.8774 (mmt) cc_final: 0.8534 (mmt) REVERT: a 312 LEU cc_start: 0.9126 (pp) cc_final: 0.8834 (tt) REVERT: a 409 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: a 453 MET cc_start: 0.8651 (mmm) cc_final: 0.8442 (mmm) REVERT: a 514 MET cc_start: 0.8845 (mtm) cc_final: 0.8442 (mtp) REVERT: b 434 MET cc_start: 0.8893 (mmp) cc_final: 0.8105 (tmt) REVERT: c 63 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7859 (mmpt) REVERT: c 80 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8993 (tm) REVERT: c 116 PRO cc_start: 0.5237 (Cg_exo) cc_final: 0.4818 (Cg_endo) REVERT: d 24 TRP cc_start: 0.8803 (p90) cc_final: 0.8588 (p90) REVERT: e 55 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8752 (tm-30) REVERT: e 59 MET cc_start: 0.5468 (mmt) cc_final: 0.5049 (mmt) REVERT: e 71 ARG cc_start: 0.9204 (ptp-110) cc_final: 0.8535 (ptp90) REVERT: e 82 ASP cc_start: 0.7756 (m-30) cc_final: 0.7322 (m-30) REVERT: f 746 MET cc_start: 0.8746 (mpp) cc_final: 0.8333 (mmt) REVERT: f 805 TRP cc_start: 0.8263 (m-10) cc_final: 0.7654 (m100) REVERT: f 812 MET cc_start: 0.8522 (tmm) cc_final: 0.8181 (tmt) REVERT: f 819 TYR cc_start: 0.7218 (t80) cc_final: 0.6506 (t80) REVERT: m 41 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8384 (mtp85) REVERT: m 78 GLU cc_start: 0.9444 (tp30) cc_final: 0.8700 (pp20) REVERT: m 101 ASP cc_start: 0.9151 (t70) cc_final: 0.8852 (t70) REVERT: m 105 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9151 (tm) outliers start: 125 outliers final: 60 residues processed: 480 average time/residue: 0.7238 time to fit residues: 426.0235 Evaluate side-chains 433 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain M residue 249 LYS Chi-restraints excluded: chain M residue 264 ASP Chi-restraints excluded: chain M residue 310 LEU Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain a residue 139 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 298 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 303 THR Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 515 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 226 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 175 ASP Chi-restraints excluded: chain e residue 183 VAL Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 910 LEU Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 285 optimal weight: 0.5980 chunk 352 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 HIS M 459 HIS d 87 ASN ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS ** f 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.103693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068085 restraints weight = 145642.438| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.23 r_work: 0.3047 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43049 Z= 0.184 Angle : 0.605 11.096 58745 Z= 0.314 Chirality : 0.040 0.201 6521 Planarity : 0.004 0.069 7028 Dihedral : 16.695 140.417 6901 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.09 % Allowed : 26.11 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.12), residues: 4775 helix: 2.51 (0.12), residues: 1972 sheet: 0.53 (0.18), residues: 765 loop : -0.25 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG d 3 TYR 0.026 0.001 TYR D 177 PHE 0.021 0.001 PHE a 448 TRP 0.021 0.001 TRP f 805 HIS 0.007 0.001 HIS b 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (43049) covalent geometry : angle 0.60517 / 0.31 (58745) hydrogen bonds : bond 0.04189 / 2.76 ( 2122) hydrogen bonds : angle 4.15682 / 2.99 ( 5945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 371 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8976 (ptpp) cc_final: 0.8760 (ptmm) REVERT: A 312 LEU cc_start: 0.8748 (mm) cc_final: 0.8401 (tt) REVERT: B 16 VAL cc_start: 0.9127 (m) cc_final: 0.8917 (t) REVERT: B 20 MET cc_start: 0.7562 (mtt) cc_final: 0.7132 (pmm) REVERT: C 47 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: C 152 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: C 165 GLN cc_start: 0.9095 (tt0) cc_final: 0.8659 (tp40) REVERT: C 180 LYS cc_start: 0.9387 (ttpp) cc_final: 0.9161 (tmmt) REVERT: C 297 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8865 (tp) REVERT: D 112 ASN cc_start: 0.9158 (m-40) cc_final: 0.8404 (t0) REVERT: D 157 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8667 (p0) REVERT: E 157 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8643 (p0) REVERT: E 165 CYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8562 (p) REVERT: F 61 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8986 (t) REVERT: F 263 MET cc_start: 0.7479 (ptp) cc_final: 0.7256 (ptp) REVERT: F 371 MET cc_start: 0.8184 (ttt) cc_final: 0.7710 (mtt) REVERT: F 783 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7758 (t0) REVERT: G 191 LYS cc_start: 0.9144 (pttt) cc_final: 0.8888 (ptmm) REVERT: H 191 LYS cc_start: 0.8863 (tppt) cc_final: 0.8469 (tppt) REVERT: M 33 TYR cc_start: 0.6839 (t80) cc_final: 0.6472 (t80) REVERT: M 138 MET cc_start: 0.8722 (tpp) cc_final: 0.8292 (tpt) REVERT: M 255 TYR cc_start: 0.9181 (t80) cc_final: 0.8901 (t80) REVERT: a 135 MET cc_start: 0.8775 (mmt) cc_final: 0.8436 (mmt) REVERT: a 312 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8833 (tt) REVERT: a 409 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: a 453 MET cc_start: 0.8680 (mmm) cc_final: 0.8462 (mmm) REVERT: a 514 MET cc_start: 0.8881 (mtm) cc_final: 0.8471 (mtp) REVERT: b 14 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8058 (tpt) REVERT: b 434 MET cc_start: 0.8879 (mmp) cc_final: 0.8095 (tmt) REVERT: b 534 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8816 (tttp) REVERT: c 80 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8945 (tm) REVERT: c 116 PRO cc_start: 0.5270 (Cg_exo) cc_final: 0.4831 (Cg_endo) REVERT: d 24 TRP cc_start: 0.8840 (p90) cc_final: 0.8534 (p90) REVERT: d 72 LYS cc_start: 0.9471 (ttpt) cc_final: 0.9116 (ptmm) REVERT: e 55 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: e 59 MET cc_start: 0.5330 (mmt) cc_final: 0.4894 (mmm) REVERT: e 71 ARG cc_start: 0.9222 (ptp-110) cc_final: 0.8561 (ptp90) REVERT: e 82 ASP cc_start: 0.7807 (m-30) cc_final: 0.7363 (m-30) REVERT: f 746 MET cc_start: 0.8788 (mpp) cc_final: 0.8508 (mmt) REVERT: f 805 TRP cc_start: 0.8227 (m-10) cc_final: 0.7691 (m100) REVERT: f 812 MET cc_start: 0.8552 (tmm) cc_final: 0.8217 (tmt) REVERT: f 819 TYR cc_start: 0.7175 (t80) cc_final: 0.6634 (t80) REVERT: m 71 MET cc_start: 0.7877 (tpp) cc_final: 0.7547 (tpp) REVERT: m 78 GLU cc_start: 0.9380 (tp30) cc_final: 0.8614 (pp20) REVERT: m 101 ASP cc_start: 0.9191 (t70) cc_final: 0.8903 (t70) REVERT: m 105 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9136 (tm) outliers start: 133 outliers final: 71 residues processed: 473 average time/residue: 0.7388 time to fit residues: 428.8273 Evaluate side-chains 446 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 360 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain M residue 249 LYS Chi-restraints excluded: chain M residue 264 ASP Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain a residue 139 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 298 THR Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 14 MET Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 303 THR Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 436 SER Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain b residue 534 LYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 226 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 183 VAL Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 882 PHE Chi-restraints excluded: chain f residue 910 LEU Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 105 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 461 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 215 optimal weight: 0.1980 chunk 204 optimal weight: 10.0000 chunk 371 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 405 optimal weight: 0.5980 chunk 283 optimal weight: 0.0980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 HIS a 423 GLN b 99 GLN b 119 GLN d 87 ASN ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS ** f 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.104868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.069591 restraints weight = 139460.090| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 4.22 r_work: 0.3073 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43049 Z= 0.124 Angle : 0.592 10.407 58745 Z= 0.307 Chirality : 0.039 0.167 6521 Planarity : 0.004 0.073 7028 Dihedral : 16.633 166.440 6901 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.65 % Allowed : 26.49 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.12), residues: 4775 helix: 2.58 (0.12), residues: 1968 sheet: 0.54 (0.18), residues: 770 loop : -0.18 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 81 TYR 0.028 0.001 TYR D 129 PHE 0.023 0.001 PHE f 766 TRP 0.030 0.001 TRP M 82 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (43049) covalent geometry : angle 0.59243 / 0.31 (58745) hydrogen bonds : bond 0.03859 / 2.54 ( 2122) hydrogen bonds : angle 4.05039 / 2.92 ( 5945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 380 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8949 (tpp) cc_final: 0.8674 (tpp) REVERT: A 265 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8738 (ptmm) REVERT: A 312 LEU cc_start: 0.8732 (mm) cc_final: 0.8379 (tt) REVERT: A 422 ASP cc_start: 0.8248 (p0) cc_final: 0.8010 (p0) REVERT: B 16 VAL cc_start: 0.9103 (m) cc_final: 0.8893 (t) REVERT: B 20 MET cc_start: 0.7579 (mtt) cc_final: 0.7231 (pmm) REVERT: B 296 CYS cc_start: 0.8930 (m) cc_final: 0.8136 (p) REVERT: B 416 TYR cc_start: 0.7783 (p90) cc_final: 0.7426 (p90) REVERT: C 152 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: C 163 GLU cc_start: 0.9292 (tm-30) cc_final: 0.9074 (tm-30) REVERT: C 165 GLN cc_start: 0.9087 (tt0) cc_final: 0.8684 (tp40) REVERT: C 180 LYS cc_start: 0.9398 (ttpp) cc_final: 0.9156 (tmmt) REVERT: C 297 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8844 (tp) REVERT: D 157 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8680 (p0) REVERT: E 59 MET cc_start: 0.8745 (ttm) cc_final: 0.8449 (ttt) REVERT: E 157 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8598 (p0) REVERT: E 165 CYS cc_start: 0.9028 (t) cc_final: 0.8525 (p) REVERT: F 61 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9003 (t) REVERT: F 263 MET cc_start: 0.7452 (ptp) cc_final: 0.7203 (ptp) REVERT: F 371 MET cc_start: 0.8095 (ttt) cc_final: 0.7581 (mtt) REVERT: F 783 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7724 (t0) REVERT: G 191 LYS cc_start: 0.9119 (pttt) cc_final: 0.8863 (ptmm) REVERT: H 183 GLU cc_start: 0.8404 (tp30) cc_final: 0.8191 (tp30) REVERT: H 191 LYS cc_start: 0.8923 (tppt) cc_final: 0.8411 (tppt) REVERT: M 33 TYR cc_start: 0.6792 (t80) cc_final: 0.6473 (t80) REVERT: M 138 MET cc_start: 0.8702 (tpp) cc_final: 0.8285 (tpt) REVERT: M 255 TYR cc_start: 0.9154 (t80) cc_final: 0.8892 (t80) REVERT: a 134 MET cc_start: 0.9243 (tmm) cc_final: 0.8836 (tmm) REVERT: a 135 MET cc_start: 0.8695 (mmt) cc_final: 0.8363 (mmt) REVERT: a 312 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8827 (tt) REVERT: a 409 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: a 514 MET cc_start: 0.8854 (mtm) cc_final: 0.8470 (mtp) REVERT: b 99 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8329 (mm110) REVERT: b 434 MET cc_start: 0.8895 (mmp) cc_final: 0.8101 (tmt) REVERT: b 534 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8788 (tttp) REVERT: c 116 PRO cc_start: 0.5038 (Cg_exo) cc_final: 0.4722 (Cg_endo) REVERT: c 167 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7982 (t80) REVERT: d 72 LYS cc_start: 0.9469 (ttpt) cc_final: 0.9120 (ptmm) REVERT: e 71 ARG cc_start: 0.9207 (ptp-110) cc_final: 0.8563 (ptp90) REVERT: e 82 ASP cc_start: 0.7734 (m-30) cc_final: 0.7299 (m-30) REVERT: e 157 ASP cc_start: 0.9107 (p0) cc_final: 0.8850 (p0) REVERT: f 743 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.7779 (ttp) REVERT: f 746 MET cc_start: 0.8804 (mpp) cc_final: 0.8556 (mpp) REVERT: f 805 TRP cc_start: 0.8174 (m-10) cc_final: 0.7684 (m100) REVERT: f 812 MET cc_start: 0.8468 (tmm) cc_final: 0.8132 (tmt) REVERT: f 819 TYR cc_start: 0.7208 (t80) cc_final: 0.3448 (t80) REVERT: f 848 HIS cc_start: 0.9460 (OUTLIER) cc_final: 0.9249 (m90) REVERT: m 41 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8379 (mmm-85) REVERT: m 94 CYS cc_start: 0.0154 (OUTLIER) cc_final: -0.0709 (m) REVERT: m 101 ASP cc_start: 0.9194 (t70) cc_final: 0.8927 (t70) outliers start: 114 outliers final: 63 residues processed: 465 average time/residue: 0.6956 time to fit residues: 397.2117 Evaluate side-chains 433 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 357 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain M residue 249 LYS Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain a residue 139 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 298 THR Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 303 THR Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain b residue 534 LYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 226 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 175 ASP Chi-restraints excluded: chain e residue 183 VAL Chi-restraints excluded: chain f residue 743 MET Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 882 PHE Chi-restraints excluded: chain f residue 910 LEU Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 94 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 162 optimal weight: 0.8980 chunk 472 optimal weight: 0.7980 chunk 170 optimal weight: 0.3980 chunk 255 optimal weight: 0.8980 chunk 310 optimal weight: 3.9990 chunk 206 optimal weight: 40.0000 chunk 350 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 HIS M 441 GLN c 6 GLN d 87 ASN e 145 GLN ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS ** f 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.104204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.068365 restraints weight = 182043.088| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.54 r_work: 0.3007 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43049 Z= 0.151 Angle : 0.609 11.440 58745 Z= 0.313 Chirality : 0.040 0.341 6521 Planarity : 0.004 0.082 7028 Dihedral : 16.664 177.716 6901 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.83 % Allowed : 26.72 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.12), residues: 4775 helix: 2.55 (0.12), residues: 1970 sheet: 0.50 (0.18), residues: 773 loop : -0.20 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG d 71 TYR 0.041 0.001 TYR f 819 PHE 0.029 0.001 PHE B 107 TRP 0.032 0.001 TRP M 82 HIS 0.009 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (43049) covalent geometry : angle 0.60909 / 0.31 (58745) hydrogen bonds : bond 0.03963 / 2.62 ( 2122) hydrogen bonds : angle 4.06758 / 2.93 ( 5945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 364 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8753 (ptmm) REVERT: A 312 LEU cc_start: 0.8730 (mm) cc_final: 0.8367 (tt) REVERT: A 422 ASP cc_start: 0.8502 (p0) cc_final: 0.8238 (p0) REVERT: A 423 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8191 (mm-40) REVERT: B 296 CYS cc_start: 0.9017 (m) cc_final: 0.8185 (p) REVERT: C 163 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9078 (tm-30) REVERT: C 165 GLN cc_start: 0.9092 (tt0) cc_final: 0.8690 (tp40) REVERT: C 180 LYS cc_start: 0.9384 (ttpp) cc_final: 0.9137 (tmmt) REVERT: C 297 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8876 (tp) REVERT: D 71 ARG cc_start: 0.9207 (ttm170) cc_final: 0.8863 (ttm110) REVERT: D 157 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8688 (p0) REVERT: E 59 MET cc_start: 0.8757 (ttm) cc_final: 0.8427 (ttt) REVERT: E 144 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8911 (tp) REVERT: E 157 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8681 (p0) REVERT: E 165 CYS cc_start: 0.9087 (t) cc_final: 0.8572 (p) REVERT: F 61 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9012 (t) REVERT: F 263 MET cc_start: 0.5586 (ptp) cc_final: 0.5233 (ptp) REVERT: F 371 MET cc_start: 0.8119 (ttt) cc_final: 0.7561 (mtt) REVERT: F 681 ARG cc_start: 0.8796 (mmp80) cc_final: 0.8566 (mmm160) REVERT: F 783 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7734 (t0) REVERT: G 191 LYS cc_start: 0.9115 (pttt) cc_final: 0.8846 (ptmm) REVERT: H 183 GLU cc_start: 0.8428 (tp30) cc_final: 0.8221 (tp30) REVERT: H 191 LYS cc_start: 0.8936 (tppt) cc_final: 0.8434 (tppt) REVERT: M 33 TYR cc_start: 0.6891 (t80) cc_final: 0.6539 (t80) REVERT: M 255 TYR cc_start: 0.9174 (t80) cc_final: 0.8897 (t80) REVERT: a 134 MET cc_start: 0.9269 (tmm) cc_final: 0.9068 (tmm) REVERT: a 135 MET cc_start: 0.8719 (mmt) cc_final: 0.8418 (mmt) REVERT: a 312 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8822 (tt) REVERT: a 409 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: a 514 MET cc_start: 0.8889 (mtm) cc_final: 0.8483 (mtp) REVERT: b 14 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8040 (tpt) REVERT: b 434 MET cc_start: 0.8951 (mmp) cc_final: 0.8114 (tmt) REVERT: b 534 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8801 (tttp) REVERT: c 109 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7879 (ttt-90) REVERT: c 167 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.8017 (t80) REVERT: d 24 TRP cc_start: 0.8872 (p90) cc_final: 0.8583 (p90) REVERT: d 61 MET cc_start: 0.5779 (ttp) cc_final: 0.5246 (ptm) REVERT: d 72 LYS cc_start: 0.9482 (ttpt) cc_final: 0.9137 (ptmm) REVERT: d 150 ARG cc_start: 0.9248 (ttp80) cc_final: 0.8971 (ttp80) REVERT: d 175 ASP cc_start: 0.9357 (t70) cc_final: 0.9042 (p0) REVERT: e 59 MET cc_start: 0.5075 (mpp) cc_final: 0.4793 (mpp) REVERT: e 61 MET cc_start: 0.5407 (OUTLIER) cc_final: 0.5107 (mmt) REVERT: e 71 ARG cc_start: 0.9224 (ptp-110) cc_final: 0.8585 (ptp90) REVERT: e 82 ASP cc_start: 0.7771 (m-30) cc_final: 0.7312 (m-30) REVERT: e 157 ASP cc_start: 0.9047 (p0) cc_final: 0.8822 (p0) REVERT: f 743 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7921 (ttp) REVERT: f 746 MET cc_start: 0.8850 (mpp) cc_final: 0.8547 (mpp) REVERT: f 764 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8612 (t) REVERT: f 805 TRP cc_start: 0.8239 (m-10) cc_final: 0.7730 (m100) REVERT: f 812 MET cc_start: 0.8480 (tmm) cc_final: 0.8159 (tmt) REVERT: f 823 TYR cc_start: 0.7591 (p90) cc_final: 0.7208 (p90) REVERT: f 848 HIS cc_start: 0.9459 (OUTLIER) cc_final: 0.9237 (m90) REVERT: f 882 PHE cc_start: 0.4719 (OUTLIER) cc_final: 0.4380 (t80) REVERT: m 94 CYS cc_start: 0.0143 (OUTLIER) cc_final: -0.0755 (m) REVERT: m 101 ASP cc_start: 0.9190 (t70) cc_final: 0.8946 (t70) outliers start: 122 outliers final: 73 residues processed: 460 average time/residue: 0.6982 time to fit residues: 395.0512 Evaluate side-chains 450 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 360 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain M residue 249 LYS Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain a residue 139 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 298 THR Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 14 MET Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 303 THR Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain b residue 534 LYS Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 226 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 183 VAL Chi-restraints excluded: chain f residue 743 MET Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 764 SER Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 882 PHE Chi-restraints excluded: chain f residue 910 LEU Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 44 ARG Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 94 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 428 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 476 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 33 optimal weight: 0.0070 chunk 181 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 386 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS F 258 HIS d 87 ASN ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.104758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069247 restraints weight = 171718.402| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.57 r_work: 0.3051 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 43049 Z= 0.128 Angle : 0.622 12.930 58745 Z= 0.318 Chirality : 0.040 0.254 6521 Planarity : 0.004 0.086 7028 Dihedral : 16.624 168.300 6901 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.34 % Allowed : 27.41 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.12), residues: 4775 helix: 2.54 (0.12), residues: 1970 sheet: 0.54 (0.18), residues: 773 loop : -0.18 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG d 71 TYR 0.032 0.001 TYR D 129 PHE 0.029 0.001 PHE B 107 TRP 0.035 0.001 TRP M 82 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (43049) covalent geometry : angle 0.62243 / 0.32 (58745) hydrogen bonds : bond 0.03809 / 2.51 ( 2122) hydrogen bonds : angle 4.05465 / 2.93 ( 5945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 374 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8697 (ptmm) REVERT: A 312 LEU cc_start: 0.8712 (mm) cc_final: 0.8350 (tt) REVERT: A 422 ASP cc_start: 0.8462 (p0) cc_final: 0.8184 (p0) REVERT: A 423 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8250 (mm-40) REVERT: B 296 CYS cc_start: 0.8997 (m) cc_final: 0.8170 (p) REVERT: B 416 TYR cc_start: 0.7540 (p90) cc_final: 0.7165 (p90) REVERT: C 86 ASP cc_start: 0.8159 (p0) cc_final: 0.7760 (p0) REVERT: C 163 GLU cc_start: 0.9272 (tm-30) cc_final: 0.9042 (tm-30) REVERT: C 165 GLN cc_start: 0.9085 (tt0) cc_final: 0.8714 (tp40) REVERT: C 180 LYS cc_start: 0.9383 (ttpp) cc_final: 0.9140 (tmmt) REVERT: D 71 ARG cc_start: 0.9193 (ttm170) cc_final: 0.8843 (ttm110) REVERT: D 157 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8680 (p0) REVERT: E 59 MET cc_start: 0.8673 (ttm) cc_final: 0.8419 (ttt) REVERT: E 144 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8901 (tp) REVERT: E 157 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8641 (p0) REVERT: E 165 CYS cc_start: 0.9045 (t) cc_final: 0.8526 (p) REVERT: F 61 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9013 (t) REVERT: F 263 MET cc_start: 0.5293 (ptp) cc_final: 0.4830 (ptp) REVERT: F 371 MET cc_start: 0.8163 (ttt) cc_final: 0.7607 (mtt) REVERT: F 783 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7750 (t0) REVERT: G 191 LYS cc_start: 0.9099 (pttt) cc_final: 0.8839 (ptmm) REVERT: H 183 GLU cc_start: 0.8424 (tp30) cc_final: 0.8214 (tp30) REVERT: H 191 LYS cc_start: 0.8939 (tppt) cc_final: 0.8421 (tppt) REVERT: M 33 TYR cc_start: 0.6964 (t80) cc_final: 0.6623 (t80) REVERT: M 87 MET cc_start: 0.7444 (ppp) cc_final: 0.6826 (mpt) REVERT: M 138 MET cc_start: 0.8728 (tpp) cc_final: 0.8276 (tpt) REVERT: M 255 TYR cc_start: 0.9165 (t80) cc_final: 0.8920 (t80) REVERT: a 134 MET cc_start: 0.9266 (tmm) cc_final: 0.9062 (tmm) REVERT: a 135 MET cc_start: 0.8740 (mmt) cc_final: 0.8408 (mmt) REVERT: a 168 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8986 (tt) REVERT: a 312 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8805 (tt) REVERT: a 409 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8532 (m-80) REVERT: a 514 MET cc_start: 0.8879 (mtm) cc_final: 0.8489 (mtp) REVERT: b 14 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8008 (tpt) REVERT: b 434 MET cc_start: 0.8949 (mmp) cc_final: 0.8065 (tmt) REVERT: b 534 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8745 (tttp) REVERT: c 167 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.8032 (t80) REVERT: c 212 MET cc_start: 0.9198 (mmm) cc_final: 0.8938 (mmm) REVERT: d 24 TRP cc_start: 0.8912 (p90) cc_final: 0.8607 (p90) REVERT: d 72 LYS cc_start: 0.9479 (ttpt) cc_final: 0.9112 (ptmm) REVERT: d 175 ASP cc_start: 0.9336 (t70) cc_final: 0.9016 (p0) REVERT: e 59 MET cc_start: 0.5199 (mpp) cc_final: 0.4848 (mpp) REVERT: e 71 ARG cc_start: 0.9223 (ptp-110) cc_final: 0.8593 (ptp90) REVERT: e 82 ASP cc_start: 0.7765 (m-30) cc_final: 0.7306 (m-30) REVERT: f 743 MET cc_start: 0.8786 (ttm) cc_final: 0.7940 (ttp) REVERT: f 764 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8562 (t) REVERT: f 805 TRP cc_start: 0.8161 (m-10) cc_final: 0.7685 (m100) REVERT: f 812 MET cc_start: 0.8458 (tmm) cc_final: 0.8148 (tmt) REVERT: f 848 HIS cc_start: 0.9440 (OUTLIER) cc_final: 0.9206 (m90) REVERT: f 882 PHE cc_start: 0.4954 (OUTLIER) cc_final: 0.4542 (t80) REVERT: m 36 GLU cc_start: 0.8122 (tp30) cc_final: 0.7484 (tp30) REVERT: m 94 CYS cc_start: 0.0322 (OUTLIER) cc_final: -0.0566 (m) REVERT: m 101 ASP cc_start: 0.9164 (t70) cc_final: 0.8924 (t70) outliers start: 101 outliers final: 69 residues processed: 452 average time/residue: 0.7483 time to fit residues: 414.5882 Evaluate side-chains 439 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 355 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain M residue 249 LYS Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain a residue 139 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 298 THR Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 14 MET Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 303 THR Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain b residue 534 LYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 226 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 183 VAL Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 764 SER Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 882 PHE Chi-restraints excluded: chain f residue 910 LEU Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 44 ARG Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 94 CYS Chi-restraints excluded: chain m residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 444 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 426 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 396 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 HIS d 87 ASN ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.103846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.069409 restraints weight = 162795.288| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 4.55 r_work: 0.3021 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 43049 Z= 0.174 Angle : 0.644 15.002 58745 Z= 0.329 Chirality : 0.041 0.298 6521 Planarity : 0.004 0.084 7028 Dihedral : 16.681 164.070 6901 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.32 % Allowed : 27.34 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.12), residues: 4775 helix: 2.51 (0.12), residues: 1972 sheet: 0.49 (0.18), residues: 781 loop : -0.20 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG d 71 TYR 0.032 0.001 TYR D 129 PHE 0.026 0.001 PHE f 742 TRP 0.036 0.001 TRP M 82 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (43049) covalent geometry : angle 0.64443 / 0.33 (58745) hydrogen bonds : bond 0.04013 / 2.65 ( 2122) hydrogen bonds : angle 4.10419 / 2.96 ( 5945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 360 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8941 (ptpp) cc_final: 0.8729 (ptmm) REVERT: A 312 LEU cc_start: 0.8725 (mm) cc_final: 0.8365 (tt) REVERT: A 422 ASP cc_start: 0.8464 (p0) cc_final: 0.8183 (p0) REVERT: A 423 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8276 (mm-40) REVERT: B 296 CYS cc_start: 0.9057 (m) cc_final: 0.8217 (p) REVERT: B 331 MET cc_start: 0.8879 (mtt) cc_final: 0.8510 (mtt) REVERT: B 416 TYR cc_start: 0.7581 (p90) cc_final: 0.7208 (p90) REVERT: C 163 GLU cc_start: 0.9298 (tm-30) cc_final: 0.9085 (tm-30) REVERT: C 165 GLN cc_start: 0.9108 (tt0) cc_final: 0.8723 (tp40) REVERT: D 71 ARG cc_start: 0.9218 (ttm170) cc_final: 0.8876 (ttm110) REVERT: D 157 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8713 (p0) REVERT: D 192 ARG cc_start: 0.9183 (mmm160) cc_final: 0.8925 (mmm160) REVERT: E 144 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8905 (tp) REVERT: E 157 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8638 (p0) REVERT: E 165 CYS cc_start: 0.9097 (t) cc_final: 0.8569 (p) REVERT: F 61 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9003 (t) REVERT: F 263 MET cc_start: -0.0028 (ptp) cc_final: -0.0313 (ptp) REVERT: F 343 MET cc_start: 0.5272 (pmt) cc_final: 0.4837 (mmt) REVERT: F 371 MET cc_start: 0.8009 (ttt) cc_final: 0.7354 (mtt) REVERT: F 783 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7772 (t0) REVERT: G 191 LYS cc_start: 0.9106 (pttt) cc_final: 0.8859 (ptmm) REVERT: H 183 GLU cc_start: 0.8417 (tp30) cc_final: 0.8204 (tp30) REVERT: H 191 LYS cc_start: 0.8941 (tppt) cc_final: 0.8454 (tppt) REVERT: M 33 TYR cc_start: 0.7026 (t80) cc_final: 0.6679 (t80) REVERT: M 87 MET cc_start: 0.7384 (ppp) cc_final: 0.6759 (mpt) REVERT: M 138 MET cc_start: 0.8749 (tpp) cc_final: 0.8248 (tpt) REVERT: M 255 TYR cc_start: 0.9174 (t80) cc_final: 0.8929 (t80) REVERT: a 134 MET cc_start: 0.9271 (tmm) cc_final: 0.9013 (tmm) REVERT: a 135 MET cc_start: 0.8681 (mmt) cc_final: 0.8277 (mmt) REVERT: a 168 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9000 (tt) REVERT: a 312 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8809 (tt) REVERT: a 409 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: a 448 PHE cc_start: 0.8671 (t80) cc_final: 0.8449 (t80) REVERT: a 514 MET cc_start: 0.8891 (mtm) cc_final: 0.8482 (mtp) REVERT: b 14 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8054 (tpt) REVERT: b 368 ARG cc_start: 0.8557 (ttm110) cc_final: 0.8013 (tpt90) REVERT: b 434 MET cc_start: 0.8964 (mmp) cc_final: 0.8109 (tmt) REVERT: c 167 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.8060 (t80) REVERT: d 24 TRP cc_start: 0.8921 (p90) cc_final: 0.8605 (p90) REVERT: d 72 LYS cc_start: 0.9489 (ttpt) cc_final: 0.9118 (ptmm) REVERT: d 175 ASP cc_start: 0.9344 (t70) cc_final: 0.9021 (p0) REVERT: e 61 MET cc_start: 0.4878 (mpt) cc_final: 0.4565 (mpt) REVERT: e 71 ARG cc_start: 0.9231 (ptp-110) cc_final: 0.8600 (ptp90) REVERT: e 82 ASP cc_start: 0.7812 (m-30) cc_final: 0.7274 (m-30) REVERT: f 746 MET cc_start: 0.8643 (mpp) cc_final: 0.8326 (mmt) REVERT: f 764 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8570 (t) REVERT: f 805 TRP cc_start: 0.8266 (m-10) cc_final: 0.7737 (m100) REVERT: f 812 MET cc_start: 0.8528 (tmm) cc_final: 0.8221 (tmt) REVERT: f 848 HIS cc_start: 0.9431 (OUTLIER) cc_final: 0.9198 (m90) REVERT: f 882 PHE cc_start: 0.4627 (OUTLIER) cc_final: 0.4405 (t80) REVERT: m 36 GLU cc_start: 0.8147 (tp30) cc_final: 0.7559 (tp30) REVERT: m 71 MET cc_start: 0.6884 (tmm) cc_final: 0.6588 (tpt) REVERT: m 78 GLU cc_start: 0.9409 (tp30) cc_final: 0.8650 (pp20) REVERT: m 101 ASP cc_start: 0.9170 (t70) cc_final: 0.8917 (t70) outliers start: 100 outliers final: 71 residues processed: 438 average time/residue: 0.7073 time to fit residues: 380.6466 Evaluate side-chains 441 residues out of total 4306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 357 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 776 GLU Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 848 HIS Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain M residue 249 LYS Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 298 THR Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 14 MET Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 303 THR Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 226 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 55 GLU Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 175 ASP Chi-restraints excluded: chain e residue 183 VAL Chi-restraints excluded: chain f residue 747 CYS Chi-restraints excluded: chain f residue 764 SER Chi-restraints excluded: chain f residue 765 TYR Chi-restraints excluded: chain f residue 788 THR Chi-restraints excluded: chain f residue 848 HIS Chi-restraints excluded: chain f residue 882 PHE Chi-restraints excluded: chain f residue 910 LEU Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 44 ARG Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 94 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 69 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 317 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 472 optimal weight: 0.0970 chunk 132 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 HIS d 87 ASN e 145 GLN ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 816 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.104092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069833 restraints weight = 159253.709| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.22 r_work: 0.3047 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43049 Z= 0.149 Angle : 0.640 16.640 58745 Z= 0.327 Chirality : 0.040 0.297 6521 Planarity : 0.004 0.084 7028 Dihedral : 16.688 159.136 6901 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.37 % Allowed : 27.32 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.12), residues: 4775 helix: 2.48 (0.12), residues: 1978 sheet: 0.54 (0.18), residues: 771 loop : -0.20 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG d 71 TYR 0.032 0.001 TYR D 129 PHE 0.023 0.001 PHE f 742 TRP 0.037 0.001 TRP M 82 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (43049) covalent geometry : angle 0.64023 / 0.33 (58745) hydrogen bonds : bond 0.03968 / 2.61 ( 2122) hydrogen bonds : angle 4.09486 / 2.96 ( 5945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23346.10 seconds wall clock time: 396 minutes 1.34 seconds (23761.34 seconds total)