Starting phenix.real_space_refine on Tue Sep 15 05:10:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ziy_11231/09_2026/6ziy_11231.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ziy_11231/09_2026/6ziy_11231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ziy_11231/09_2026/6ziy_11231.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ziy_11231/09_2026/6ziy_11231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ziy_11231/09_2026/6ziy_11231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ziy_11231/09_2026/6ziy_11231.map" model { file = "/net/cci-nas-00/data/ceres_data/6ziy_11231/09_2026/6ziy_11231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ziy_11231/09_2026/6ziy_11231.cif" } resolution = 4.25 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= 0.000 sd= 0.045 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 Fe 32 7.16 5 P 3 5.49 5 S 180 5.16 5 C 23646 2.51 5 N 6005 2.21 5 O 6235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 361 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36101 Number of models: 1 Model: "" Number of chains: 20 Chain: "1" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3417 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 405} Chain: "2" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1406 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "3" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5876 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 53, 'TRANS': 700} Chain breaks: 2 Chain: "4" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3067 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 353} Chain: "5" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1607 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 16, 'TRANS': 179} Chain: "6" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1289 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 153} Chain: "9" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 163} Chain: "7" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1031 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "A" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "J" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1183 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "K" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 703 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'TRANS': 94} Chain: "L" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4604 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 575} Chain: "M" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3489 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain: "N" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3154 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 401} Chain: "H" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2838 Classifications: {'peptide': 353} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 333} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Unusual residues: {'FES': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2772 SG CYS 1 356 112.447 70.668 225.820 1.00 50.00 S ATOM 2792 SG CYS 1 359 116.968 72.842 227.815 1.00 50.00 S ATOM 3102 SG CYS 1 400 111.557 70.732 230.725 1.00 50.00 S ATOM 2753 SG CYS 1 353 115.669 66.764 228.638 1.00 50.00 S ATOM 4091 SG CYS 2 83 127.129 73.877 245.643 1.00 50.00 S ATOM 4123 SG CYS 2 88 128.001 76.134 247.898 1.00 50.00 S ATOM 4394 SG CYS 2 124 122.450 74.150 245.755 1.00 50.00 S ATOM 4418 SG CYS 2 128 122.272 76.914 248.527 1.00 50.00 S ATOM 5640 SG CYS 3 128 119.826 66.759 205.395 1.00 50.00 S ATOM 5584 SG CYS 3 119 124.624 69.285 204.047 1.00 50.00 S ATOM 5604 SG CYS 3 122 124.847 63.347 204.723 1.00 50.00 S ATOM 6083 SG CYS 3 184 114.716 61.249 214.755 1.00 50.00 S ATOM 6059 SG CYS 3 181 120.559 62.365 215.869 1.00 50.00 S ATOM 6109 SG CYS 3 187 116.962 56.821 216.256 1.00 50.00 S ATOM 6445 SG CYS 3 230 118.872 59.448 210.936 1.00 50.00 S ATOM 6652 SG CYS 3 256 110.563 40.981 198.999 1.00 50.00 S ATOM 6918 SG CYS 3 291 112.370 40.978 204.894 1.00 50.00 S ATOM 6695 SG CYS 3 263 106.882 43.048 202.014 1.00 50.00 S ATOM 6671 SG CYS 3 259 108.051 37.016 203.233 1.00 50.00 S ATOM 5085 SG CYS 3 34 108.455 65.630 217.307 1.00 50.00 S ATOM 5163 SG CYS 3 45 110.033 68.960 215.522 1.00 50.00 S ATOM 5188 SG CYS 3 48 104.740 70.246 215.458 1.00 50.00 S ATOM 5320 SG CYS 3 83 104.307 67.157 217.162 1.00 50.00 S ATOM 16119 SG CYS 6 111 124.512 73.316 168.623 1.00 50.00 S ATOM 15614 SG CYS 6 46 129.088 76.164 165.725 1.00 50.00 S ATOM 15608 SG CYS 6 45 124.000 78.349 167.619 1.00 50.00 S ATOM 16328 SG CYS 6 140 128.156 76.570 172.135 1.00 50.00 S ATOM 17432 SG CYS 9 101 128.166 74.739 180.368 1.00 50.00 S ATOM 17407 SG CYS 9 98 131.477 71.468 177.659 1.00 50.00 S ATOM 17450 SG CYS 9 104 131.307 72.888 184.151 1.00 50.00 S ATOM 17129 SG CYS 9 63 127.179 69.311 181.597 1.00 50.00 S ATOM 17479 SG CYS 9 108 134.275 71.374 192.572 1.00 50.00 S ATOM 17108 SG CYS 9 59 131.190 68.295 188.888 1.00 50.00 S ATOM 17070 SG CYS 9 53 136.512 66.140 192.495 1.00 50.00 S ATOM 17088 SG CYS 9 56 130.557 68.129 194.407 1.00 50.00 S Time building chain proxies: 7.10, per 1000 atoms: 0.20 Number of scatterers: 36101 At special positions: 0 Unit cell: (175.44, 132.44, 283.8, 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) Fe 32 26.01 S 180 16.00 P 3 15.00 O 6235 8.00 N 6005 7.00 C 23646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 2 144 " - pdb=" SG CYS 2 172 " distance=2.03 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: 2.91 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 201 " pdb="FE2 FES 2 201 " - pdb=" SG CYS 2 124 " pdb="FE2 FES 2 201 " - pdb=" SG CYS 2 128 " pdb="FE1 FES 2 201 " - pdb=" SG CYS 2 88 " pdb="FE1 FES 2 201 " - pdb=" SG CYS 2 83 " pdb=" FES 3 804 " pdb="FE2 FES 3 804 " - pdb=" SG CYS 3 83 " pdb="FE2 FES 3 804 " - pdb=" SG CYS 3 48 " pdb="FE1 FES 3 804 " - pdb=" SG CYS 3 45 " pdb="FE1 FES 3 804 " - pdb=" SG CYS 3 34 " pdb=" SF4 1 501 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 353 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 400 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 356 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 115 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 122 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 119 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 128 " pdb=" SF4 3 802 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 230 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 181 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 187 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 184 " pdb=" SF4 3 803 " pdb="FE4 SF4 3 803 " - pdb=" SG CYS 3 259 " pdb="FE2 SF4 3 803 " - pdb=" SG CYS 3 291 " pdb="FE3 SF4 3 803 " - pdb=" SG CYS 3 263 " pdb="FE1 SF4 3 803 " - pdb=" SG CYS 3 256 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 140 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 45 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 46 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 111 " pdb=" SF4 9 201 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 63 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 104 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 101 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 98 " pdb=" SF4 9 202 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 56 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 59 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 53 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 108 " Number of angles added : 93 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8414 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 24 sheets defined 59.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain '1' and resid 28 through 34 Processing helix chain '1' and resid 38 through 47 removed outlier: 4.422A pdb=" N LYS 1 46 " --> pdb=" O LYS 1 42 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 61 removed outlier: 3.710A pdb=" N VAL 1 53 " --> pdb=" O THR 1 49 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL 1 57 " --> pdb=" O VAL 1 53 " (cutoff:3.500A) Processing helix chain '1' and resid 71 through 76 Processing helix chain '1' and resid 102 through 110 removed outlier: 4.159A pdb=" N ILE 1 106 " --> pdb=" O LYS 1 102 " (cutoff:3.500A) Processing helix chain '1' and resid 110 through 125 removed outlier: 4.037A pdb=" N LEU 1 114 " --> pdb=" O VAL 1 110 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 155 Processing helix chain '1' and resid 179 through 183 Processing helix chain '1' and resid 184 through 194 removed outlier: 3.514A pdb=" N MET 1 189 " --> pdb=" O GLU 1 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN 1 190 " --> pdb=" O THR 1 186 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 214 Processing helix chain '1' and resid 221 through 226 Processing helix chain '1' and resid 226 through 234 removed outlier: 3.697A pdb=" N ILE 1 230 " --> pdb=" O SER 1 226 " (cutoff:3.500A) Processing helix chain '1' and resid 234 through 240 removed outlier: 4.192A pdb=" N GLN 1 240 " --> pdb=" O ASP 1 236 " (cutoff:3.500A) Processing helix chain '1' and resid 271 through 277 Processing helix chain '1' and resid 303 through 308 Processing helix chain '1' and resid 316 through 320 Processing helix chain '1' and resid 336 through 352 removed outlier: 3.508A pdb=" N ALA 1 340 " --> pdb=" O SER 1 336 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS 1 350 " --> pdb=" O ARG 1 346 " (cutoff:3.500A) Processing helix chain '1' and resid 356 through 361 Processing helix chain '1' and resid 366 through 375 Processing helix chain '1' and resid 381 through 391 removed outlier: 3.887A pdb=" N LEU 1 391 " --> pdb=" O LEU 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 391 through 396 removed outlier: 3.983A pdb=" N GLY 1 396 " --> pdb=" O PRO 1 392 " (cutoff:3.500A) Processing helix chain '1' and resid 401 through 417 removed outlier: 3.585A pdb=" N ALA 1 405 " --> pdb=" O PRO 1 401 " (cutoff:3.500A) Proline residue: 1 409 - end of helix removed outlier: 3.627A pdb=" N LEU 1 414 " --> pdb=" O VAL 1 410 " (cutoff:3.500A) Processing helix chain '1' and resid 418 through 427 Processing helix chain '2' and resid 7 through 17 removed outlier: 3.522A pdb=" N LEU 2 11 " --> pdb=" O LYS 2 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS 2 17 " --> pdb=" O GLU 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 22 through 25 Processing helix chain '2' and resid 26 through 39 removed outlier: 3.552A pdb=" N GLU 2 38 " --> pdb=" O VAL 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 54 removed outlier: 3.820A pdb=" N ILE 2 46 " --> pdb=" O ARG 2 42 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 65 removed outlier: 3.587A pdb=" N VAL 2 60 " --> pdb=" O THR 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 85 through 91 Processing helix chain '2' and resid 92 through 105 removed outlier: 3.780A pdb=" N LEU 2 96 " --> pdb=" O GLY 2 92 " (cutoff:3.500A) Processing helix chain '2' and resid 127 through 131 Processing helix chain '2' and resid 146 through 159 removed outlier: 3.539A pdb=" N ALA 2 159 " --> pdb=" O ALA 2 155 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 26 removed outlier: 3.643A pdb=" N ALA 3 22 " --> pdb=" O SER 3 18 " (cutoff:3.500A) Processing helix chain '3' and resid 81 through 85 removed outlier: 3.522A pdb=" N THR 3 85 " --> pdb=" O SER 3 82 " (cutoff:3.500A) Processing helix chain '3' and resid 97 through 113 Processing helix chain '3' and resid 128 through 138 Processing helix chain '3' and resid 178 through 181 Processing helix chain '3' and resid 185 through 194 Processing helix chain '3' and resid 205 through 209 removed outlier: 3.734A pdb=" N THR 3 209 " --> pdb=" O GLY 3 206 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 224 No H-bonds generated for 'chain '3' and resid 222 through 224' Processing helix chain '3' and resid 225 through 230 Processing helix chain '3' and resid 239 through 241 No H-bonds generated for 'chain '3' and resid 239 through 241' Processing helix chain '3' and resid 245 through 249 removed outlier: 3.541A pdb=" N MET 3 249 " --> pdb=" O ASN 3 246 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 296 Processing helix chain '3' and resid 298 through 302 Processing helix chain '3' and resid 321 through 333 Processing helix chain '3' and resid 350 through 364 Processing helix chain '3' and resid 387 through 392 Processing helix chain '3' and resid 401 through 406 Processing helix chain '3' and resid 408 through 418 removed outlier: 3.793A pdb=" N ARG 3 418 " --> pdb=" O SER 3 414 " (cutoff:3.500A) Processing helix chain '3' and resid 456 through 462 removed outlier: 3.593A pdb=" N MET 3 459 " --> pdb=" O ALA 3 456 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS 3 460 " --> pdb=" O PRO 3 457 " (cutoff:3.500A) Processing helix chain '3' and resid 472 through 482 removed outlier: 3.742A pdb=" N ILE 3 476 " --> pdb=" O GLU 3 472 " (cutoff:3.500A) Processing helix chain '3' and resid 487 through 500 Processing helix chain '3' and resid 508 through 513 removed outlier: 4.204A pdb=" N LEU 3 512 " --> pdb=" O GLY 3 508 " (cutoff:3.500A) Processing helix chain '3' and resid 514 through 528 removed outlier: 3.888A pdb=" N GLU 3 526 " --> pdb=" O ARG 3 522 " (cutoff:3.500A) Processing helix chain '3' and resid 540 through 547 Processing helix chain '3' and resid 573 through 578 Processing helix chain '3' and resid 606 through 610 Processing helix chain '3' and resid 636 through 648 removed outlier: 3.517A pdb=" N GLU 3 646 " --> pdb=" O ALA 3 642 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA 3 647 " --> pdb=" O LEU 3 643 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU 3 648 " --> pdb=" O LEU 3 644 " (cutoff:3.500A) Processing helix chain '3' and resid 656 through 668 Processing helix chain '3' and resid 700 through 704 removed outlier: 4.007A pdb=" N ALA 3 704 " --> pdb=" O ALA 3 701 " (cutoff:3.500A) Processing helix chain '3' and resid 707 through 712 removed outlier: 4.473A pdb=" N ALA 3 711 " --> pdb=" O LYS 3 707 " (cutoff:3.500A) Processing helix chain '3' and resid 719 through 726 Processing helix chain '4' and resid 65 through 70 removed outlier: 3.746A pdb=" N THR 4 69 " --> pdb=" O GLY 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 71 through 73 No H-bonds generated for 'chain '4' and resid 71 through 73' Processing helix chain '4' and resid 76 through 85 removed outlier: 4.226A pdb=" N THR 4 82 " --> pdb=" O ILE 4 79 " (cutoff:3.500A) Proline residue: 4 83 - end of helix Processing helix chain '4' and resid 89 through 106 removed outlier: 4.141A pdb=" N HIS 4 93 " --> pdb=" O HIS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 110 through 140 removed outlier: 3.588A pdb=" N GLU 4 114 " --> pdb=" O PRO 4 110 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU 4 140 " --> pdb=" O GLY 4 136 " (cutoff:3.500A) Processing helix chain '4' and resid 144 through 165 removed outlier: 4.097A pdb=" N TYR 4 148 " --> pdb=" O THR 4 144 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG 4 153 " --> pdb=" O ALA 4 149 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL 4 163 " --> pdb=" O LEU 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 209 removed outlier: 3.535A pdb=" N GLU 4 189 " --> pdb=" O GLU 4 185 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 4 196 " --> pdb=" O LYS 4 192 " (cutoff:3.500A) Proline residue: 4 198 - end of helix removed outlier: 3.909A pdb=" N LEU 4 207 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE 4 208 " --> pdb=" O TYR 4 204 " (cutoff:3.500A) Processing helix chain '4' and resid 211 through 219 removed outlier: 3.515A pdb=" N GLU 4 216 " --> pdb=" O PRO 4 212 " (cutoff:3.500A) Processing helix chain '4' and resid 225 through 232 Processing helix chain '4' and resid 238 through 243 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 256 through 260 Processing helix chain '4' and resid 271 through 296 removed outlier: 3.730A pdb=" N ILE 4 280 " --> pdb=" O MET 4 276 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS 4 288 " --> pdb=" O ARG 4 284 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE 4 289 " --> pdb=" O GLU 4 285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU 4 295 " --> pdb=" O LYS 4 291 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG 4 296 " --> pdb=" O GLN 4 292 " (cutoff:3.500A) Processing helix chain '4' and resid 320 through 333 removed outlier: 3.545A pdb=" N VAL 4 324 " --> pdb=" O SER 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 372 through 378 Processing helix chain '4' and resid 380 through 385 Processing helix chain '4' and resid 389 through 401 removed outlier: 3.836A pdb=" N VAL 4 394 " --> pdb=" O VAL 4 390 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA 4 395 " --> pdb=" O PRO 4 391 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE 4 397 " --> pdb=" O MET 4 393 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP 4 401 " --> pdb=" O ILE 4 397 " (cutoff:3.500A) Processing helix chain '4' and resid 403 through 409 removed outlier: 3.865A pdb=" N VAL 4 407 " --> pdb=" O VAL 4 403 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 14 removed outlier: 3.585A pdb=" N GLU 5 9 " --> pdb=" O ARG 5 5 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 44 Processing helix chain '5' and resid 110 through 122 removed outlier: 3.749A pdb=" N LEU 5 114 " --> pdb=" O SER 5 110 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG 5 116 " --> pdb=" O ASN 5 112 " (cutoff:3.500A) Processing helix chain '5' and resid 166 through 171 removed outlier: 4.001A pdb=" N PHE 5 170 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG 5 171 " --> pdb=" O PRO 5 167 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 166 through 171' Processing helix chain '5' and resid 186 through 191 Processing helix chain '6' and resid 21 through 35 removed outlier: 3.605A pdb=" N SER 6 35 " --> pdb=" O GLY 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 46 through 53 removed outlier: 3.836A pdb=" N SER 6 53 " --> pdb=" O GLU 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 71 through 75 removed outlier: 3.715A pdb=" N GLN 6 74 " --> pdb=" O SER 6 71 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA 6 75 " --> pdb=" O PRO 6 72 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 71 through 75' Processing helix chain '6' and resid 85 through 87 No H-bonds generated for 'chain '6' and resid 85 through 87' Processing helix chain '6' and resid 88 through 98 Processing helix chain '6' and resid 109 through 114 Processing helix chain '6' and resid 126 through 130 Processing helix chain '6' and resid 143 through 159 removed outlier: 3.527A pdb=" N LEU 6 147 " --> pdb=" O ARG 6 143 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 19 removed outlier: 4.088A pdb=" N ALA 9 7 " --> pdb=" O LEU 9 3 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU 9 10 " --> pdb=" O LEU 9 6 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR 9 13 " --> pdb=" O SER 9 9 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 9 19 " --> pdb=" O LYS 9 15 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 63 removed outlier: 3.782A pdb=" N ALA 9 61 " --> pdb=" O SER 9 57 " (cutoff:3.500A) Processing helix chain '9' and resid 102 through 108 Processing helix chain '9' and resid 125 through 128 Processing helix chain '9' and resid 134 through 136 No H-bonds generated for 'chain '9' and resid 134 through 136' Processing helix chain '9' and resid 143 through 153 removed outlier: 3.602A pdb=" N ARG 9 152 " --> pdb=" O ARG 9 148 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 28 removed outlier: 4.184A pdb=" N GLU 7 8 " --> pdb=" O SER 7 4 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA 7 12 " --> pdb=" O GLU 7 8 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 42 Processing helix chain '7' and resid 111 through 127 Processing helix chain 'A' and resid 4 through 31 Processing helix chain 'A' and resid 59 through 84 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 88 through 114 Processing helix chain 'J' and resid 2 through 22 removed outlier: 3.536A pdb=" N GLY J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU J 7 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 46 Processing helix chain 'J' and resid 48 through 60 removed outlier: 3.849A pdb=" N GLY J 52 " --> pdb=" O ALA J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 74 removed outlier: 3.574A pdb=" N LEU J 74 " --> pdb=" O VAL J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 87 Processing helix chain 'J' and resid 88 through 109 removed outlier: 4.443A pdb=" N LEU J 92 " --> pdb=" O ARG J 88 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 135 through 158 removed outlier: 3.501A pdb=" N VAL J 157 " --> pdb=" O ALA J 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 removed outlier: 3.730A pdb=" N ALA K 8 " --> pdb=" O LEU K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 50 removed outlier: 4.075A pdb=" N ALA K 48 " --> pdb=" O GLY K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 79 removed outlier: 3.978A pdb=" N VAL K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 20 removed outlier: 3.579A pdb=" N THR L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE L 7 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Proline residue: L 10 - end of helix removed outlier: 3.506A pdb=" N PHE L 14 " --> pdb=" O PRO L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 50 removed outlier: 3.518A pdb=" N PHE L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 47 " --> pdb=" O LEU L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 95 removed outlier: 3.635A pdb=" N MET L 95 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 120 Processing helix chain 'L' and resid 123 through 143 Processing helix chain 'L' and resid 149 through 179 removed outlier: 5.717A pdb=" N ALA L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG L 163 " --> pdb=" O PHE L 159 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY L 165 " --> pdb=" O VAL L 161 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 193 Processing helix chain 'L' and resid 198 through 217 removed outlier: 3.926A pdb=" N GLY L 215 " --> pdb=" O LEU L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 231 removed outlier: 3.517A pdb=" N MET L 230 " --> pdb=" O PRO L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 242 Processing helix chain 'L' and resid 245 through 256 removed outlier: 3.827A pdb=" N VAL L 250 " --> pdb=" O VAL L 246 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE L 253 " --> pdb=" O GLY L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 261 Processing helix chain 'L' and resid 263 through 286 removed outlier: 3.585A pdb=" N SER L 267 " --> pdb=" O LEU L 263 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 310 removed outlier: 4.056A pdb=" N SER L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 340 removed outlier: 3.845A pdb=" N PHE L 327 " --> pdb=" O PHE L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 348 through 352 removed outlier: 3.727A pdb=" N LYS L 351 " --> pdb=" O ASP L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 375 removed outlier: 3.630A pdb=" N HIS L 365 " --> pdb=" O GLN L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.619A pdb=" N TRP L 383 " --> pdb=" O LEU L 379 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU L 393 " --> pdb=" O LEU L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 426 removed outlier: 3.564A pdb=" N TYR L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL L 404 " --> pdb=" O VAL L 400 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY L 405 " --> pdb=" O GLY L 401 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU L 408 " --> pdb=" O VAL L 404 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 411 " --> pdb=" O LEU L 407 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA L 417 " --> pdb=" O THR L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 456 Proline residue: L 445 - end of helix removed outlier: 3.529A pdb=" N VAL L 454 " --> pdb=" O ALA L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 460 removed outlier: 4.414A pdb=" N ALA L 460 " --> pdb=" O GLY L 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 457 through 460' Processing helix chain 'L' and resid 469 through 474 Processing helix chain 'L' and resid 488 through 512 removed outlier: 3.677A pdb=" N GLY L 492 " --> pdb=" O GLY L 488 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU L 493 " --> pdb=" O ALA L 489 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU L 502 " --> pdb=" O ALA L 498 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP L 506 " --> pdb=" O LEU L 502 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY L 508 " --> pdb=" O GLY L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 530 removed outlier: 4.298A pdb=" N ALA L 523 " --> pdb=" O ALA L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 542 removed outlier: 3.547A pdb=" N ALA L 537 " --> pdb=" O TYR L 533 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU L 541 " --> pdb=" O ALA L 537 " (cutoff:3.500A) Processing helix chain 'L' and resid 542 through 580 removed outlier: 3.514A pdb=" N LEU L 546 " --> pdb=" O ILE L 542 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Processing helix chain 'L' and resid 585 through 604 removed outlier: 3.594A pdb=" N TYR L 589 " --> pdb=" O TYR L 585 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 18 Proline residue: M 9 - end of helix Processing helix chain 'M' and resid 22 through 43 removed outlier: 3.708A pdb=" N VAL M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 60 Processing helix chain 'M' and resid 68 through 89 removed outlier: 4.450A pdb=" N LEU M 73 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE M 74 " --> pdb=" O LEU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 112 Processing helix chain 'M' and resid 114 through 125 Processing helix chain 'M' and resid 125 through 135 removed outlier: 3.781A pdb=" N ALA M 129 " --> pdb=" O ALA M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 169 Proline residue: M 158 - end of helix removed outlier: 4.329A pdb=" N ALA M 161 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA M 162 " --> pdb=" O PRO M 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.753A pdb=" N LEU M 180 " --> pdb=" O LEU M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 203 removed outlier: 4.017A pdb=" N ALA M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 211 Processing helix chain 'M' and resid 213 through 221 removed outlier: 3.541A pdb=" N ASN M 221 " --> pdb=" O PHE M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 removed outlier: 3.531A pdb=" N GLY M 231 " --> pdb=" O ALA M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 244 Processing helix chain 'M' and resid 244 through 249 Processing helix chain 'M' and resid 249 through 277 removed outlier: 4.121A pdb=" N GLN M 255 " --> pdb=" O GLU M 251 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY M 258 " --> pdb=" O ALA M 254 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU M 259 " --> pdb=" O GLN M 255 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA M 268 " --> pdb=" O ALA M 264 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA M 277 " --> pdb=" O TRP M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 302 Processing helix chain 'M' and resid 304 through 335 removed outlier: 3.719A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY M 323 " --> pdb=" O GLY M 319 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU M 325 " --> pdb=" O TYR M 321 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG M 335 " --> pdb=" O ARG M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 351 removed outlier: 3.564A pdb=" N SER M 350 " --> pdb=" O GLY M 346 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA M 351 " --> pdb=" O LEU M 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 346 through 351' Processing helix chain 'M' and resid 353 through 367 Processing helix chain 'M' and resid 372 through 388 removed outlier: 4.613A pdb=" N GLY M 376 " --> pdb=" O SER M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 396 removed outlier: 3.616A pdb=" N ALA M 392 " --> pdb=" O SER M 388 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 397 through 415 removed outlier: 3.861A pdb=" N ALA M 401 " --> pdb=" O LEU M 397 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR M 413 " --> pdb=" O ALA M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 446 removed outlier: 4.018A pdb=" N GLY M 431 " --> pdb=" O GLY M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 447 through 452 removed outlier: 3.826A pdb=" N PHE M 450 " --> pdb=" O PRO M 447 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA M 451 " --> pdb=" O GLY M 448 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG M 452 " --> pdb=" O TYR M 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 447 through 452' Processing helix chain 'M' and resid 453 through 464 removed outlier: 4.701A pdb=" N LEU M 457 " --> pdb=" O GLY M 453 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU M 459 " --> pdb=" O HIS M 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 17 removed outlier: 3.880A pdb=" N LEU N 15 " --> pdb=" O VAL N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 42 removed outlier: 3.703A pdb=" N VAL N 25 " --> pdb=" O PRO N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 77 removed outlier: 3.511A pdb=" N LEU N 76 " --> pdb=" O TRP N 72 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL N 77 " --> pdb=" O THR N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 100 removed outlier: 5.590A pdb=" N VAL N 88 " --> pdb=" O PHE N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 122 Proline residue: N 117 - end of helix removed outlier: 3.634A pdb=" N ALA N 120 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 159 removed outlier: 3.643A pdb=" N GLU N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA N 133 " --> pdb=" O GLY N 129 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY N 156 " --> pdb=" O ALA N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 188 removed outlier: 3.522A pdb=" N ALA N 173 " --> pdb=" O GLY N 169 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 179 " --> pdb=" O ALA N 175 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU N 180 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY N 182 " --> pdb=" O LEU N 178 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU N 183 " --> pdb=" O LEU N 179 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA N 187 " --> pdb=" O LEU N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 203 removed outlier: 4.311A pdb=" N ASP N 198 " --> pdb=" O PHE N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 213 Processing helix chain 'N' and resid 213 through 225 removed outlier: 3.958A pdb=" N ARG N 225 " --> pdb=" O ALA N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 248 removed outlier: 3.507A pdb=" N ALA N 234 " --> pdb=" O PRO N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 251 No H-bonds generated for 'chain 'N' and resid 249 through 251' Processing helix chain 'N' and resid 253 through 273 removed outlier: 3.518A pdb=" N ALA N 266 " --> pdb=" O SER N 262 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU N 271 " --> pdb=" O GLY N 267 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA N 272 " --> pdb=" O TYR N 268 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU N 273 " --> pdb=" O MET N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 303 Processing helix chain 'N' and resid 308 through 313 Processing helix chain 'N' and resid 314 through 319 removed outlier: 3.542A pdb=" N LYS N 318 " --> pdb=" O GLY N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 319 through 335 Processing helix chain 'N' and resid 339 through 356 removed outlier: 4.272A pdb=" N TRP N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA N 348 " --> pdb=" O GLY N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 371 removed outlier: 4.017A pdb=" N LEU N 361 " --> pdb=" O ALA N 357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA N 369 " --> pdb=" O LEU N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 371 through 380 Processing helix chain 'N' and resid 381 through 384 Processing helix chain 'N' and resid 395 through 415 removed outlier: 3.758A pdb=" N ARG N 399 " --> pdb=" O PRO N 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 423 removed outlier: 5.561A pdb=" N LEU N 420 " --> pdb=" O GLY N 417 " (cutoff:3.500A) Proline residue: N 421 - end of helix Processing helix chain 'H' and resid 9 through 43 removed outlier: 3.576A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 67 removed outlier: 3.574A pdb=" N ILE H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 95 Proline residue: H 86 - end of helix removed outlier: 3.724A pdb=" N SER H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA H 93 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 144 removed outlier: 4.247A pdb=" N TYR H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA H 132 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY H 144 " --> pdb=" O GLY H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 178 removed outlier: 3.517A pdb=" N LEU H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY H 167 " --> pdb=" O GLU H 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU H 168 " --> pdb=" O LEU H 164 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA H 172 " --> pdb=" O LEU H 168 " (cutoff:3.500A) Proline residue: H 173 - end of helix removed outlier: 3.730A pdb=" N LEU H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 192 Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.770A pdb=" N TYR H 198 " --> pdb=" O TRP H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 211 removed outlier: 3.603A pdb=" N VAL H 205 " --> pdb=" O PRO H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 214 No H-bonds generated for 'chain 'H' and resid 212 through 214' Processing helix chain 'H' and resid 238 through 264 removed outlier: 3.769A pdb=" N ALA H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) Proline residue: H 260 - end of helix Processing helix chain 'H' and resid 276 through 297 removed outlier: 3.520A pdb=" N TRP H 297 " --> pdb=" O ILE H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 312 removed outlier: 3.545A pdb=" N PHE H 312 " --> pdb=" O PHE H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 330 Processing helix chain 'H' and resid 334 through 351 removed outlier: 3.724A pdb=" N LEU H 340 " --> pdb=" O TYR H 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 171 through 175 removed outlier: 3.649A pdb=" N VAL 1 134 " --> pdb=" O HIS 1 174 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS 1 87 " --> pdb=" O ALA 1 127 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL 1 129 " --> pdb=" O HIS 1 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 249 through 254 removed outlier: 3.601A pdb=" N TYR 1 252 " --> pdb=" O TYR 1 264 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY 1 262 " --> pdb=" O ILE 1 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 300 through 301 removed outlier: 6.735A pdb=" N ILE 1 331 " --> pdb=" O GLN 1 288 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE 1 290 " --> pdb=" O ILE 1 329 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE 1 329 " --> pdb=" O ILE 1 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 117 through 122 removed outlier: 3.563A pdb=" N SER 2 118 " --> pdb=" O TYR 2 78 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE 2 134 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL 2 136 " --> pdb=" O PRO 2 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 9 through 12 removed outlier: 7.949A pdb=" N VAL 3 93 " --> pdb=" O ARG 3 3 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS 3 5 " --> pdb=" O VAL 3 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 168 through 171 removed outlier: 6.236A pdb=" N VAL 3 174 " --> pdb=" O LEU 3 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 201 through 202 removed outlier: 3.774A pdb=" N ASP 3 201 " --> pdb=" O GLY 3 212 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY 3 212 " --> pdb=" O ASP 3 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '3' and resid 250 through 255 removed outlier: 6.998A pdb=" N ARG 3 270 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU 3 274 " --> pdb=" O ARG 3 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 317 through 319 removed outlier: 5.883A pdb=" N VAL 3 583 " --> pdb=" O VAL 3 600 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU 3 602 " --> pdb=" O VAL 3 583 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET 3 585 " --> pdb=" O LEU 3 602 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLY 3 342 " --> pdb=" O TYR 3 567 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP 3 370 " --> pdb=" O LEU 3 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 464 through 465 removed outlier: 4.127A pdb=" N ILE 3 464 " --> pdb=" O MET 3 448 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU 3 397 " --> pdb=" O ILE 3 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 612 through 615 Processing sheet with id=AB3, first strand: chain '3' and resid 734 through 738 removed outlier: 7.171A pdb=" N ALA 3 714 " --> pdb=" O ARG 3 746 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL 3 748 " --> pdb=" O ALA 3 714 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU 3 716 " --> pdb=" O VAL 3 748 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLU 3 715 " --> pdb=" O SER 3 761 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR 3 693 " --> pdb=" O LEU 3 760 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA 3 762 " --> pdb=" O TYR 3 693 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG 3 695 " --> pdb=" O ALA 3 762 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 27 through 30 removed outlier: 3.678A pdb=" N GLU 4 54 " --> pdb=" O THR 4 46 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER 4 48 " --> pdb=" O VAL 4 52 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL 4 52 " --> pdb=" O SER 4 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 340 through 342 Processing sheet with id=AB6, first strand: chain '4' and resid 340 through 342 removed outlier: 4.087A pdb=" N GLY 4 354 " --> pdb=" O ARG 4 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 48 through 56 removed outlier: 5.404A pdb=" N LEU 5 49 " --> pdb=" O VAL 5 75 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL 5 75 " --> pdb=" O LEU 5 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP 5 51 " --> pdb=" O GLU 5 73 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL 5 70 " --> pdb=" O VAL 5 92 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '5' and resid 157 through 158 Processing sheet with id=AB9, first strand: chain '6' and resid 38 through 42 removed outlier: 3.663A pdb=" N VAL 6 135 " --> pdb=" O VAL 6 105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '9' and resid 31 through 32 removed outlier: 6.183A pdb=" N VAL 9 31 " --> pdb=" O VAL 9 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain '9' and resid 39 through 43 removed outlier: 4.855A pdb=" N ARG 9 40 " --> pdb=" O GLY 9 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '9' and resid 68 through 74 removed outlier: 6.637A pdb=" N TYR 9 69 " --> pdb=" O TYR 9 91 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR 9 91 " --> pdb=" O TYR 9 69 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU 9 71 " --> pdb=" O LYS 9 89 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '7' and resid 30 through 36 removed outlier: 6.375A pdb=" N THR 7 56 " --> pdb=" O GLU 7 34 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP 7 36 " --> pdb=" O ILE 7 54 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE 7 54 " --> pdb=" O ASP 7 36 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N MET 7 55 " --> pdb=" O ASP 7 71 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP 7 71 " --> pdb=" O MET 7 55 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA 7 57 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU 7 69 " --> pdb=" O ALA 7 57 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU 7 59 " --> pdb=" O PHE 7 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 57 Processing sheet with id=AC6, first strand: chain 'M' and resid 50 through 56 removed outlier: 5.527A pdb=" N GLN M 52 " --> pdb=" O PHE M 65 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE M 65 " --> pdb=" O GLN M 52 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TRP M 63 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL M 61 " --> pdb=" O LEU M 56 " (cutoff:3.500A) 1875 hydrogen bonds defined for protein. 5397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.44: 17687 1.44 - 1.67: 19065 1.67 - 1.91: 256 1.91 - 2.14: 0 2.14 - 2.38: 92 Bond restraints: 37100 Sorted by residual: bond pdb=" CD GLU 3 192 " pdb=" OE2 GLU 3 192 " ideal model delta sigma weight residual 1.249 1.398 -0.149 1.90e-02 2.77e+03 6.14e+01 bond pdb=" CG ASP L 386 " pdb=" OD2 ASP L 386 " ideal model delta sigma weight residual 1.249 1.397 -0.148 1.90e-02 2.77e+03 6.07e+01 bond pdb=" CD GLU H 225 " pdb=" OE2 GLU H 225 " ideal model delta sigma weight residual 1.249 1.394 -0.145 1.90e-02 2.77e+03 5.84e+01 bond pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sigma weight residual 1.249 1.393 -0.144 1.90e-02 2.77e+03 5.76e+01 bond pdb=" CD GLU K 32 " pdb=" OE2 GLU K 32 " ideal model delta sigma weight residual 1.249 1.393 -0.144 1.90e-02 2.77e+03 5.75e+01 ... (remaining 37095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 44973 3.83 - 7.66: 5188 7.66 - 11.48: 362 11.48 - 15.31: 12 15.31 - 19.14: 2 Bond angle restraints: 50537 Sorted by residual: angle pdb=" C THR 1 72 " pdb=" CA THR 1 72 " pdb=" CB THR 1 72 " ideal model delta sigma weight residual 110.74 91.60 19.14 1.66e+00 3.63e-01 1.33e+02 angle pdb=" CA PHE H 286 " pdb=" CB PHE H 286 " pdb=" CG PHE H 286 " ideal model delta sigma weight residual 113.80 103.22 10.58 1.00e+00 1.00e+00 1.12e+02 angle pdb=" CA PHE 9 100 " pdb=" CB PHE 9 100 " pdb=" CG PHE 9 100 " ideal model delta sigma weight residual 113.80 103.93 9.87 1.00e+00 1.00e+00 9.75e+01 angle pdb=" CA ALA N 165 " pdb=" C ALA N 165 " pdb=" N PRO N 166 " ideal model delta sigma weight residual 117.69 126.26 -8.57 9.30e-01 1.16e+00 8.50e+01 angle pdb=" C ILE 1 331 " pdb=" N PRO 1 332 " pdb=" CA PRO 1 332 " ideal model delta sigma weight residual 120.31 129.11 -8.80 9.80e-01 1.04e+00 8.07e+01 ... (remaining 50532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 21003 34.00 - 68.00: 558 68.00 - 102.00: 94 102.00 - 136.00: 0 136.00 - 170.00: 1 Dihedral angle restraints: 21656 sinusoidal: 8429 harmonic: 13227 Sorted by residual: dihedral pdb=" C THR 1 72 " pdb=" N THR 1 72 " pdb=" CA THR 1 72 " pdb=" CB THR 1 72 " ideal model delta harmonic sigma weight residual -122.00 -98.94 -23.06 0 2.50e+00 1.60e-01 8.51e+01 dihedral pdb=" CA THR H 217 " pdb=" C THR H 217 " pdb=" N PRO H 218 " pdb=" CA PRO H 218 " ideal model delta harmonic sigma weight residual 180.00 137.44 42.56 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" N CYS 9 104 " pdb=" C CYS 9 104 " pdb=" CA CYS 9 104 " pdb=" CB CYS 9 104 " ideal model delta harmonic sigma weight residual 122.80 143.66 -20.86 0 2.50e+00 1.60e-01 6.96e+01 ... (remaining 21653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.213: 5644 4.213 - 8.426: 0 8.426 - 12.639: 0 12.639 - 16.852: 0 16.852 - 21.065: 28 Chirality restraints: 5672 Sorted by residual: chirality pdb="FE3 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.51 -21.06 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4 9 202 " pdb=" S1 SF4 9 202 " pdb=" S2 SF4 9 202 " pdb=" S4 SF4 9 202 " both_signs ideal model delta sigma weight residual False -10.55 10.23 -20.78 2.00e-01 2.50e+01 1.08e+04 chirality pdb="FE3 SF4 3 803 " pdb=" S1 SF4 3 803 " pdb=" S2 SF4 3 803 " pdb=" S4 SF4 3 803 " both_signs ideal model delta sigma weight residual False -10.55 10.20 -20.75 2.00e-01 2.50e+01 1.08e+04 ... (remaining 5669 not shown) Planarity restraints: 6377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 344 " -0.276 2.00e-02 2.50e+03 1.44e-01 4.13e+02 pdb=" CG TYR M 344 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TYR M 344 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 TYR M 344 " 0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR M 344 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR M 344 " 0.066 2.00e-02 2.50e+03 pdb=" CZ TYR M 344 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR M 344 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 449 " 0.275 2.00e-02 2.50e+03 1.42e-01 4.03e+02 pdb=" CG TYR M 449 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 TYR M 449 " -0.134 2.00e-02 2.50e+03 pdb=" CD2 TYR M 449 " -0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR M 449 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR M 449 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR M 449 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR M 449 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 81 " 0.270 2.00e-02 2.50e+03 1.40e-01 3.91e+02 pdb=" CG TYR A 81 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 TYR A 81 " -0.127 2.00e-02 2.50e+03 pdb=" CD2 TYR A 81 " -0.117 2.00e-02 2.50e+03 pdb=" CE1 TYR A 81 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR A 81 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR A 81 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 81 " 0.190 2.00e-02 2.50e+03 ... (remaining 6374 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 184 2.52 - 3.11: 27549 3.11 - 3.71: 52247 3.71 - 4.30: 80233 4.30 - 4.90: 131380 Nonbonded interactions: 291593 Sorted by model distance: nonbonded pdb=" CG ARG 1 65 " pdb=" OG1 THR 1 223 " model vdw 1.919 3.440 nonbonded pdb=" CB ARG 1 65 " pdb=" OG1 THR 1 223 " model vdw 1.979 3.440 nonbonded pdb=" O2' FMN 1 502 " pdb=" O4' FMN 1 502 " model vdw 2.101 3.040 nonbonded pdb=" O1P FMN 1 502 " pdb=" O4' FMN 1 502 " model vdw 2.257 3.040 nonbonded pdb=" OG SER 1 100 " pdb=" OG1 THR 1 325 " model vdw 2.295 3.040 ... (remaining 291588 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.880 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.021 0.149 37137 Z= 1.458 Angle : 2.466 42.602 50632 Z= 1.576 Chirality : 1.393 21.065 5672 Planarity : 0.023 0.263 6377 Dihedral : 15.920 169.997 13239 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 3.45 % Allowed : 9.89 % Favored : 86.67 % Rotamer: Outliers : 3.34 % Allowed : 6.78 % Favored : 89.88 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.37 % 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: -4.76 (0.10), residues: 4612 helix: -3.09 (0.07), residues: 2383 sheet: -2.36 (0.28), residues: 236 loop : -3.23 (0.12), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 9 86 TYR 0.276 0.034 TYR M 344 PHE 0.150 0.020 PHE 4 208 TRP 0.207 0.030 TRP H 194 HIS 0.008 0.002 HIS 3 183 Details of bonding type rmsd/Z covalent geometry : bond 0.02104 / 1.46 (37100) covalent geometry : angle 2.36695 / 1.57 (50537) SS BOND : bond 0.00312 / 0.16 ( 1) SS BOND : angle 26.27756 / 15.37 ( 2) hydrogen bonds : bond 0.25150 / 16.87 ( 1871) hydrogen bonds : angle 9.26459 / 6.48 ( 5397) metal coordination : bond 0.02924 / 1.97 ( 36) metal coordination : angle 15.81978 / 11.59 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1429 time to evaluate : 1.380 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: 1 14 GLU cc_start: 0.4974 (pt0) cc_final: 0.3511 (pm20) REVERT: 1 102 LYS cc_start: 0.8484 (pttp) cc_final: 0.7829 (pttp) REVERT: 1 110 VAL cc_start: 0.8899 (m) cc_final: 0.8669 (m) REVERT: 1 215 PRO cc_start: 0.8963 (OUTLIER) cc_final: 0.8485 (Cg_endo) REVERT: 1 251 LEU cc_start: 0.9086 (mt) cc_final: 0.8672 (mt) REVERT: 1 268 MET cc_start: 0.6616 (mtp) cc_final: 0.5801 (mtp) REVERT: 1 286 PRO cc_start: 0.7761 (Cg_endo) cc_final: 0.7482 (Cg_exo) REVERT: 1 288 GLN cc_start: 0.8085 (tt0) cc_final: 0.7712 (mm110) REVERT: 1 342 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.7372 (t60) REVERT: 1 351 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8435 (mm-30) REVERT: 1 370 LEU cc_start: 0.9606 (mt) cc_final: 0.9402 (mt) REVERT: 1 407 VAL cc_start: 0.9385 (m) cc_final: 0.9180 (p) REVERT: 1 408 TRP cc_start: 0.7626 (m-10) cc_final: 0.7169 (m-10) REVERT: 2 3 PHE cc_start: 0.5934 (m-80) cc_final: 0.5424 (m-10) REVERT: 2 9 ASP cc_start: 0.6973 (m-30) cc_final: 0.6356 (t0) REVERT: 2 35 GLN cc_start: 0.8736 (tp40) cc_final: 0.8453 (tp40) REVERT: 2 36 GLN cc_start: 0.9210 (mt0) cc_final: 0.8659 (mt0) REVERT: 2 49 ILE cc_start: 0.8328 (mt) cc_final: 0.7851 (tp) REVERT: 2 71 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7124 (tp40) REVERT: 2 97 TRP cc_start: 0.8304 (t-100) cc_final: 0.7927 (t60) REVERT: 2 101 THR cc_start: 0.7374 (m) cc_final: 0.7029 (t) REVERT: 2 141 TYR cc_start: 0.7316 (m-80) cc_final: 0.6261 (m-80) REVERT: 3 37 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8174 (mtmm) REVERT: 3 47 MET cc_start: 0.8789 (mmm) cc_final: 0.8568 (tpp) REVERT: 3 82 SER cc_start: 0.9448 (m) cc_final: 0.9197 (t) REVERT: 3 109 GLU cc_start: 0.8539 (tt0) cc_final: 0.8263 (tt0) REVERT: 3 114 ASN cc_start: 0.8735 (m110) cc_final: 0.8298 (m110) REVERT: 3 133 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8611 (mmp80) REVERT: 3 184 CYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8863 (p) REVERT: 3 189 ARG cc_start: 0.9269 (ttm170) cc_final: 0.8872 (mtm110) REVERT: 3 228 ASP cc_start: 0.8188 (m-30) cc_final: 0.7945 (t0) REVERT: 3 237 ASP cc_start: 0.9013 (p0) cc_final: 0.8701 (p0) REVERT: 3 251 GLU cc_start: 0.7320 (mp0) cc_final: 0.7060 (mp0) REVERT: 3 255 THR cc_start: 0.9538 (m) cc_final: 0.9330 (t) REVERT: 3 284 GLU cc_start: 0.8045 (pt0) cc_final: 0.7475 (pt0) REVERT: 3 351 LEU cc_start: 0.8517 (mt) cc_final: 0.7737 (mp) REVERT: 3 387 LEU cc_start: 0.8077 (mt) cc_final: 0.7559 (mt) REVERT: 3 404 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7510 (mp0) REVERT: 3 459 MET cc_start: 0.8198 (mtt) cc_final: 0.7732 (mtm) REVERT: 3 535 MET cc_start: 0.6596 (mtm) cc_final: 0.6379 (mtm) REVERT: 3 558 TRP cc_start: 0.8760 (OUTLIER) cc_final: 0.7002 (p-90) REVERT: 3 567 TYR cc_start: 0.5301 (OUTLIER) cc_final: 0.4286 (t80) REVERT: 3 624 LEU cc_start: 0.9126 (mp) cc_final: 0.8877 (mp) REVERT: 3 655 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6765 (ptm160) REVERT: 3 760 LEU cc_start: 0.7950 (tp) cc_final: 0.7327 (tt) REVERT: 4 40 VAL cc_start: 0.8710 (p) cc_final: 0.8486 (p) REVERT: 4 71 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8128 (mt-10) REVERT: 4 87 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: 4 121 ASN cc_start: 0.8776 (t0) cc_final: 0.8140 (t0) REVERT: 4 171 ASN cc_start: 0.8693 (m-40) cc_final: 0.7699 (p0) REVERT: 4 194 LEU cc_start: 0.9176 (mt) cc_final: 0.8874 (mt) REVERT: 4 271 ASP cc_start: 0.7622 (m-30) cc_final: 0.7232 (m-30) REVERT: 4 315 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7847 (m170) REVERT: 4 364 MET cc_start: 0.9177 (mtm) cc_final: 0.8861 (mtm) REVERT: 4 380 SER cc_start: 0.9276 (m) cc_final: 0.9064 (t) REVERT: 5 105 THR cc_start: 0.8799 (p) cc_final: 0.8572 (p) REVERT: 5 115 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8783 (mt-10) REVERT: 5 122 PHE cc_start: 0.8121 (m-80) cc_final: 0.7718 (m-80) REVERT: 5 136 LEU cc_start: 0.8874 (mt) cc_final: 0.8667 (mp) REVERT: 5 170 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7215 (t80) REVERT: 6 94 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7618 (mtm-85) REVERT: 6 97 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8299 (mt-10) REVERT: 6 103 LYS cc_start: 0.8715 (pttt) cc_final: 0.8265 (ptpt) REVERT: 6 155 GLN cc_start: 0.8516 (tt0) cc_final: 0.8280 (tt0) REVERT: 9 14 LEU cc_start: 0.9077 (tp) cc_final: 0.8819 (tp) REVERT: 9 44 THR cc_start: 0.9168 (p) cc_final: 0.8460 (t) REVERT: 9 91 TYR cc_start: 0.8656 (t80) cc_final: 0.7359 (t80) REVERT: 9 95 MET cc_start: 0.9340 (mmt) cc_final: 0.8903 (mmm) REVERT: 9 131 TYR cc_start: 0.8466 (m-80) cc_final: 0.7817 (m-80) REVERT: 9 149 GLU cc_start: 0.8174 (tt0) cc_final: 0.7685 (mt-10) REVERT: 7 11 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6717 (mm-30) REVERT: 7 16 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8982 (tt) REVERT: 7 21 ARG cc_start: 0.8274 (mtt90) cc_final: 0.7922 (mtt180) REVERT: 7 25 GLN cc_start: 0.7093 (pt0) cc_final: 0.5333 (tp40) REVERT: A 56 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7717 (ptt-90) REVERT: A 57 PHE cc_start: 0.8332 (m-80) cc_final: 0.8054 (m-80) REVERT: A 67 LEU cc_start: 0.8305 (tp) cc_final: 0.8071 (tt) REVERT: A 72 ASP cc_start: 0.8831 (t0) cc_final: 0.8608 (t0) REVERT: A 108 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8154 (tp) REVERT: J 1 MET cc_start: 0.4260 (mmm) cc_final: 0.3721 (mmt) REVERT: J 20 VAL cc_start: 0.8729 (m) cc_final: 0.8476 (p) REVERT: J 39 LEU cc_start: 0.9349 (tp) cc_final: 0.9052 (tp) REVERT: J 43 TYR cc_start: 0.8834 (m-80) cc_final: 0.8424 (m-80) REVERT: J 96 LEU cc_start: 0.8200 (mt) cc_final: 0.7998 (mp) REVERT: J 120 LYS cc_start: 0.8514 (mtmm) cc_final: 0.7800 (mmtt) REVERT: J 135 TRP cc_start: 0.8343 (m100) cc_final: 0.8135 (m100) REVERT: K 43 VAL cc_start: 0.8918 (t) cc_final: 0.8698 (t) REVERT: K 70 VAL cc_start: 0.9433 (t) cc_final: 0.9204 (t) REVERT: K 94 ARG cc_start: 0.6296 (ptt180) cc_final: 0.4971 (ptm-80) REVERT: L 25 ARG cc_start: 0.5827 (mtm180) cc_final: 0.5529 (mmt180) REVERT: L 28 LEU cc_start: 0.6778 (tp) cc_final: 0.6339 (tp) REVERT: L 36 LEU cc_start: 0.7666 (mt) cc_final: 0.7143 (tt) REVERT: L 63 ILE cc_start: 0.7593 (mp) cc_final: 0.6960 (mp) REVERT: L 75 PHE cc_start: 0.7264 (t80) cc_final: 0.6719 (t80) REVERT: L 104 PHE cc_start: 0.8339 (t80) cc_final: 0.7768 (t80) REVERT: L 108 PHE cc_start: 0.8685 (t80) cc_final: 0.8280 (t80) REVERT: L 115 MET cc_start: 0.6435 (tpt) cc_final: 0.6171 (tpp) REVERT: L 127 MET cc_start: 0.8233 (mtp) cc_final: 0.7929 (mmt) REVERT: L 138 SER cc_start: 0.8514 (m) cc_final: 0.8262 (p) REVERT: L 225 TRP cc_start: 0.7782 (p-90) cc_final: 0.7434 (p-90) REVERT: L 333 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7118 (t80) REVERT: L 355 LEU cc_start: 0.7623 (mt) cc_final: 0.7268 (tp) REVERT: L 377 PRO cc_start: 0.6026 (Cg_exo) cc_final: 0.5656 (Cg_endo) REVERT: M 1 MET cc_start: 0.5371 (tpt) cc_final: 0.5117 (mmm) REVERT: M 33 PHE cc_start: 0.8253 (t80) cc_final: 0.7966 (t80) REVERT: M 78 ILE cc_start: 0.8604 (mt) cc_final: 0.8292 (mt) REVERT: M 98 LEU cc_start: 0.9416 (mt) cc_final: 0.8342 (mp) REVERT: M 100 LEU cc_start: 0.8866 (mt) cc_final: 0.8352 (tp) REVERT: M 109 LEU cc_start: 0.8782 (tp) cc_final: 0.8429 (tp) REVERT: M 123 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8293 (mm-30) REVERT: M 132 MET cc_start: 0.8949 (ptp) cc_final: 0.8610 (ptp) REVERT: M 208 PHE cc_start: 0.8156 (t80) cc_final: 0.7824 (t80) REVERT: M 211 HIS cc_start: 0.6785 (p90) cc_final: 0.6144 (p-80) REVERT: M 281 PHE cc_start: 0.6275 (m-80) cc_final: 0.5878 (m-80) REVERT: M 302 SER cc_start: 0.9147 (m) cc_final: 0.8788 (p) REVERT: N 114 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8263 (tt) REVERT: N 116 LEU cc_start: 0.9192 (mt) cc_final: 0.8961 (mp) REVERT: N 119 TYR cc_start: 0.8412 (m-80) cc_final: 0.8198 (m-80) REVERT: N 171 LEU cc_start: 0.9392 (tp) cc_final: 0.9009 (tp) REVERT: N 255 LYS cc_start: 0.9186 (mttt) cc_final: 0.8768 (mttt) REVERT: N 258 LEU cc_start: 0.8844 (mt) cc_final: 0.8459 (mm) REVERT: N 260 TYR cc_start: 0.8757 (m-80) cc_final: 0.8547 (m-80) REVERT: N 296 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: N 318 LYS cc_start: 0.7778 (mttm) cc_final: 0.7395 (tptp) REVERT: N 326 PHE cc_start: 0.9101 (t80) cc_final: 0.8437 (t80) REVERT: N 363 LEU cc_start: 0.8394 (mt) cc_final: 0.7828 (tt) REVERT: H 74 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8339 (t) REVERT: H 137 PHE cc_start: 0.8652 (p90) cc_final: 0.7943 (p90) REVERT: H 149 LEU cc_start: 0.8497 (tp) cc_final: 0.8185 (tp) REVERT: H 163 GLU cc_start: 0.6795 (tp30) cc_final: 0.6255 (tp30) REVERT: H 223 GLU cc_start: 0.6691 (tt0) cc_final: 0.6406 (tt0) REVERT: H 250 ILE cc_start: 0.9249 (mt) cc_final: 0.8975 (mm) REVERT: H 262 LEU cc_start: 0.9078 (mt) cc_final: 0.8799 (mt) REVERT: H 299 ARG cc_start: 0.7945 (ptp-170) cc_final: 0.6588 (ptp-170) REVERT: H 335 THR cc_start: 0.7746 (p) cc_final: 0.7443 (p) outliers start: 122 outliers final: 41 residues processed: 1506 average time/residue: 0.2321 time to fit residues: 568.9621 Evaluate side-chains 987 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 928 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 174 HIS 1 386 ASN ** 2 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 7 ASN 3 163 HIS 3 168 HIS 3 368 HIS ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 513 GLN 3 639 GLN 4 72 HIS 4 77 GLN 4 78 ASN ** 4 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 315 HIS 4 377 ASN ** 6 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 125 GLN 9 41 HIS 7 76 HIS A 60 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 GLN ** L 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 436 HIS L 544 ASN M 36 ASN ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 HIS N 60 GLN N 103 HIS N 245 ASN N 279 GLN H 192 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105276 restraints weight = 83693.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106995 restraints weight = 53744.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108815 restraints weight = 36881.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109215 restraints weight = 28954.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109389 restraints weight = 22951.286| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 37137 Z= 0.417 Angle : 2.622 54.072 50632 Z= 1.485 Chirality : 0.455 6.866 5672 Planarity : 0.007 0.104 6377 Dihedral : 7.266 165.431 5099 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.81 % Favored : 93.86 % Rotamer: Outliers : 0.22 % Allowed : 4.48 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.07 % 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: -1.95 (0.11), residues: 4612 helix: -0.31 (0.10), residues: 2439 sheet: -1.24 (0.32), residues: 228 loop : -2.61 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 587 TYR 0.049 0.002 TYR H 147 PHE 0.050 0.002 PHE L 328 TRP 0.033 0.003 TRP H 310 HIS 0.014 0.002 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01170 / 0.42 (37100) covalent geometry : angle 2.28265 / 1.48 (50537) SS BOND : bond 0.00354 / 0.19 ( 1) SS BOND : angle 3.28958 / 1.72 ( 2) hydrogen bonds : bond 0.05761 / 3.81 ( 1871) hydrogen bonds : angle 5.48570 / 3.80 ( 5397) metal coordination : bond 0.01967 / 1.37 ( 36) metal coordination : angle 30.18969 / 21.06 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1178 time to evaluate : 1.314 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: 1 14 GLU cc_start: 0.4906 (pt0) cc_final: 0.4039 (pm20) REVERT: 1 201 LEU cc_start: 0.8063 (mt) cc_final: 0.7734 (mt) REVERT: 1 268 MET cc_start: 0.7136 (mtp) cc_final: 0.6904 (ttm) REVERT: 1 270 THR cc_start: 0.8877 (p) cc_final: 0.8291 (t) REVERT: 1 311 MET cc_start: 0.8846 (mtm) cc_final: 0.8591 (mtm) REVERT: 1 370 LEU cc_start: 0.9099 (mt) cc_final: 0.8814 (tp) REVERT: 2 8 GLN cc_start: 0.7084 (mm-40) cc_final: 0.6784 (mm110) REVERT: 2 9 ASP cc_start: 0.6606 (m-30) cc_final: 0.6093 (t0) REVERT: 2 28 MET cc_start: 0.7976 (mmm) cc_final: 0.7338 (mmm) REVERT: 2 35 GLN cc_start: 0.8355 (tp40) cc_final: 0.7645 (tm-30) REVERT: 2 36 GLN cc_start: 0.9034 (mt0) cc_final: 0.8504 (mt0) REVERT: 2 61 MET cc_start: 0.8104 (tpt) cc_final: 0.7640 (tpt) REVERT: 2 69 TYR cc_start: 0.7997 (t80) cc_final: 0.7596 (t80) REVERT: 2 141 TYR cc_start: 0.7497 (m-80) cc_final: 0.5842 (m-80) REVERT: 2 151 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7177 (mt-10) REVERT: 3 47 MET cc_start: 0.8245 (mmm) cc_final: 0.7959 (tpp) REVERT: 3 82 SER cc_start: 0.9248 (m) cc_final: 0.8932 (p) REVERT: 3 113 LEU cc_start: 0.9372 (tp) cc_final: 0.9159 (tp) REVERT: 3 228 ASP cc_start: 0.8580 (m-30) cc_final: 0.8146 (t0) REVERT: 3 284 GLU cc_start: 0.8075 (pt0) cc_final: 0.7709 (pt0) REVERT: 3 397 LEU cc_start: 0.7428 (tp) cc_final: 0.7182 (tp) REVERT: 3 404 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7532 (mp0) REVERT: 3 437 ILE cc_start: 0.8355 (pt) cc_final: 0.7903 (pt) REVERT: 3 459 MET cc_start: 0.8148 (mtt) cc_final: 0.7844 (mtm) REVERT: 3 531 LYS cc_start: 0.7702 (mppt) cc_final: 0.7295 (mmtt) REVERT: 3 655 ARG cc_start: 0.8220 (mpp-170) cc_final: 0.7631 (mtp-110) REVERT: 3 771 VAL cc_start: 0.8115 (m) cc_final: 0.7913 (m) REVERT: 4 71 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8111 (mt-10) REVERT: 4 109 VAL cc_start: 0.9050 (p) cc_final: 0.8547 (m) REVERT: 4 158 ASP cc_start: 0.8816 (m-30) cc_final: 0.8445 (t0) REVERT: 4 170 HIS cc_start: 0.7479 (m-70) cc_final: 0.7143 (m90) REVERT: 4 217 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7679 (mtp180) REVERT: 4 238 SER cc_start: 0.8637 (m) cc_final: 0.8235 (p) REVERT: 4 282 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7603 (mt-10) REVERT: 4 290 ILE cc_start: 0.8729 (mt) cc_final: 0.8442 (mt) REVERT: 4 364 MET cc_start: 0.8942 (mtm) cc_final: 0.8698 (mtm) REVERT: 4 378 LEU cc_start: 0.8740 (tp) cc_final: 0.8413 (tt) REVERT: 4 380 SER cc_start: 0.9450 (m) cc_final: 0.9073 (t) REVERT: 5 17 ILE cc_start: 0.8976 (pt) cc_final: 0.8401 (mt) REVERT: 5 56 ASP cc_start: 0.8476 (t0) cc_final: 0.8046 (t0) REVERT: 5 62 ASP cc_start: 0.8915 (m-30) cc_final: 0.8701 (m-30) REVERT: 5 75 VAL cc_start: 0.8946 (t) cc_final: 0.8530 (p) REVERT: 5 105 THR cc_start: 0.9153 (p) cc_final: 0.8925 (p) REVERT: 5 106 ASP cc_start: 0.8159 (m-30) cc_final: 0.7497 (p0) REVERT: 5 113 PHE cc_start: 0.7662 (m-80) cc_final: 0.7129 (m-10) REVERT: 5 122 PHE cc_start: 0.8048 (m-80) cc_final: 0.7499 (m-80) REVERT: 5 136 LEU cc_start: 0.8977 (mt) cc_final: 0.8710 (mt) REVERT: 5 177 LYS cc_start: 0.8203 (tttm) cc_final: 0.7981 (tptm) REVERT: 6 27 LEU cc_start: 0.8773 (tp) cc_final: 0.8317 (tp) REVERT: 6 51 MET cc_start: 0.7877 (mmt) cc_final: 0.7665 (tpp) REVERT: 6 86 LYS cc_start: 0.8863 (tptt) cc_final: 0.8590 (tttt) REVERT: 6 92 MET cc_start: 0.8665 (tpp) cc_final: 0.8125 (tpp) REVERT: 6 103 LYS cc_start: 0.8793 (pttt) cc_final: 0.8508 (ptpt) REVERT: 6 117 MET cc_start: 0.9001 (ptt) cc_final: 0.8670 (ptp) REVERT: 9 3 LEU cc_start: 0.9295 (mt) cc_final: 0.8838 (tp) REVERT: 9 14 LEU cc_start: 0.9090 (tp) cc_final: 0.8849 (tp) REVERT: 9 23 THR cc_start: 0.9104 (m) cc_final: 0.8761 (t) REVERT: 9 44 THR cc_start: 0.9107 (p) cc_final: 0.8720 (t) REVERT: 9 149 GLU cc_start: 0.7951 (tt0) cc_final: 0.7551 (mm-30) REVERT: 7 90 HIS cc_start: 0.7132 (p90) cc_final: 0.6359 (t70) REVERT: 7 104 VAL cc_start: 0.8057 (m) cc_final: 0.7785 (p) REVERT: 7 107 LYS cc_start: 0.7618 (ptpp) cc_final: 0.7242 (mttm) REVERT: A 55 LYS cc_start: 0.5483 (pttt) cc_final: 0.5082 (pptt) REVERT: A 56 ARG cc_start: 0.8275 (tpp-160) cc_final: 0.7735 (ptt180) REVERT: J 7 LEU cc_start: 0.8469 (tp) cc_final: 0.8250 (tp) REVERT: J 73 LEU cc_start: 0.8883 (tp) cc_final: 0.8633 (tp) REVERT: J 115 PHE cc_start: 0.6461 (m-80) cc_final: 0.6258 (m-10) REVERT: J 135 TRP cc_start: 0.8180 (m100) cc_final: 0.7911 (m100) REVERT: J 137 PHE cc_start: 0.7925 (t80) cc_final: 0.7507 (t80) REVERT: J 144 PHE cc_start: 0.8340 (t80) cc_final: 0.8039 (t80) REVERT: K 36 ASN cc_start: 0.8278 (m-40) cc_final: 0.7532 (m-40) REVERT: K 54 GLN cc_start: 0.8314 (mt0) cc_final: 0.8044 (mp10) REVERT: L 25 ARG cc_start: 0.7175 (mtm180) cc_final: 0.5652 (mmt180) REVERT: L 75 PHE cc_start: 0.7195 (t80) cc_final: 0.6350 (t80) REVERT: L 115 MET cc_start: 0.6277 (tpt) cc_final: 0.6027 (tpt) REVERT: L 131 TRP cc_start: 0.7654 (m-10) cc_final: 0.7263 (m100) REVERT: L 134 VAL cc_start: 0.9430 (t) cc_final: 0.9098 (m) REVERT: L 138 SER cc_start: 0.8888 (m) cc_final: 0.8651 (p) REVERT: L 170 MET cc_start: 0.8156 (mtm) cc_final: 0.7728 (mtm) REVERT: L 225 TRP cc_start: 0.8053 (p-90) cc_final: 0.7721 (p-90) REVERT: L 265 ASP cc_start: 0.7898 (p0) cc_final: 0.6644 (t70) REVERT: L 316 TRP cc_start: 0.5437 (p-90) cc_final: 0.4779 (p-90) REVERT: L 331 LEU cc_start: 0.8215 (tp) cc_final: 0.7971 (tp) REVERT: L 334 LEU cc_start: 0.8573 (mp) cc_final: 0.7695 (mp) REVERT: L 355 LEU cc_start: 0.8572 (mt) cc_final: 0.7515 (tp) REVERT: L 377 PRO cc_start: 0.6879 (Cg_exo) cc_final: 0.6478 (Cg_endo) REVERT: L 415 MET cc_start: 0.8474 (mmm) cc_final: 0.8136 (mmt) REVERT: L 416 TYR cc_start: 0.8433 (p90) cc_final: 0.7941 (p90) REVERT: L 461 LEU cc_start: 0.7953 (mt) cc_final: 0.7684 (mt) REVERT: M 98 LEU cc_start: 0.9279 (mt) cc_final: 0.9033 (mp) REVERT: M 100 LEU cc_start: 0.8855 (mt) cc_final: 0.8566 (mm) REVERT: M 109 LEU cc_start: 0.9250 (tp) cc_final: 0.8756 (tp) REVERT: M 228 ASP cc_start: 0.8671 (m-30) cc_final: 0.8399 (m-30) REVERT: M 234 TYR cc_start: 0.7764 (t80) cc_final: 0.7379 (t80) REVERT: M 246 ILE cc_start: 0.8170 (mp) cc_final: 0.7866 (mt) REVERT: M 282 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8128 (mttt) REVERT: M 283 THR cc_start: 0.8086 (m) cc_final: 0.7624 (t) REVERT: M 284 LEU cc_start: 0.7913 (tp) cc_final: 0.7644 (tp) REVERT: M 285 LEU cc_start: 0.9296 (mp) cc_final: 0.8890 (mp) REVERT: M 363 LEU cc_start: 0.8718 (mt) cc_final: 0.8437 (mt) REVERT: M 377 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7589 (mm-30) REVERT: M 443 MET cc_start: 0.8775 (mtt) cc_final: 0.8243 (mtp) REVERT: M 445 VAL cc_start: 0.8868 (p) cc_final: 0.8401 (p) REVERT: N 39 SER cc_start: 0.8911 (t) cc_final: 0.8412 (p) REVERT: N 40 LEU cc_start: 0.7332 (tp) cc_final: 0.6941 (tp) REVERT: N 103 HIS cc_start: 0.7709 (t-90) cc_final: 0.7301 (t-170) REVERT: N 126 ARG cc_start: 0.6902 (mtt180) cc_final: 0.6320 (mtt-85) REVERT: N 137 PHE cc_start: 0.8405 (t80) cc_final: 0.7051 (t80) REVERT: N 198 ASP cc_start: 0.8463 (m-30) cc_final: 0.8260 (m-30) REVERT: N 201 GLN cc_start: 0.9098 (tt0) cc_final: 0.8841 (tt0) REVERT: N 326 PHE cc_start: 0.9010 (t80) cc_final: 0.8029 (t80) REVERT: N 330 MET cc_start: 0.8576 (mmp) cc_final: 0.8333 (mmp) REVERT: N 333 LEU cc_start: 0.8796 (mt) cc_final: 0.8511 (tp) REVERT: N 363 LEU cc_start: 0.7877 (mt) cc_final: 0.7221 (tt) REVERT: H 95 LEU cc_start: 0.8719 (mm) cc_final: 0.8294 (mm) REVERT: H 137 PHE cc_start: 0.8351 (p90) cc_final: 0.7443 (p90) REVERT: H 149 LEU cc_start: 0.8872 (tp) cc_final: 0.8518 (tp) REVERT: H 181 ASN cc_start: 0.7679 (m-40) cc_final: 0.7472 (t0) REVERT: H 223 GLU cc_start: 0.6630 (tt0) cc_final: 0.6159 (tt0) REVERT: H 225 GLU cc_start: 0.4591 (mt-10) cc_final: 0.4227 (mt-10) REVERT: H 246 MET cc_start: 0.7668 (ttm) cc_final: 0.7335 (ttt) REVERT: H 279 MET cc_start: 0.8550 (tpt) cc_final: 0.8031 (tpt) REVERT: H 281 LEU cc_start: 0.7908 (mt) cc_final: 0.7659 (mt) REVERT: H 337 LEU cc_start: 0.8831 (mt) cc_final: 0.8471 (tp) REVERT: H 341 SER cc_start: 0.8797 (m) cc_final: 0.8514 (p) outliers start: 8 outliers final: 3 residues processed: 1185 average time/residue: 0.2186 time to fit residues: 434.3927 Evaluate side-chains 828 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 825 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 380 optimal weight: 8.9990 chunk 427 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 243 optimal weight: 0.4980 chunk 447 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 337 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 302 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 315 HIS ** 2 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 38 HIS ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 589 HIS ** 3 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 379 GLN 6 34 ASN 6 98 GLN 6 155 GLN A 60 HIS L 433 HIS M 186 GLN ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 255 GLN M 292 HIS M 455 HIS N 60 GLN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 245 ASN ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102762 restraints weight = 83502.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104315 restraints weight = 53904.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105951 restraints weight = 38037.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106387 restraints weight = 31090.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106597 restraints weight = 24344.105| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 37137 Z= 0.414 Angle : 2.627 55.016 50632 Z= 1.482 Chirality : 0.446 6.463 5672 Planarity : 0.006 0.072 6377 Dihedral : 6.812 170.055 5099 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.35 % Favored : 93.32 % Rotamer: Outliers : 0.19 % Allowed : 4.16 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.96 (0.12), residues: 4612 helix: 0.59 (0.10), residues: 2442 sheet: -0.88 (0.32), residues: 241 loop : -2.27 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 6 57 TYR 0.029 0.002 TYR N 268 PHE 0.035 0.002 PHE J 69 TRP 0.034 0.002 TRP M 415 HIS 0.019 0.002 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01178 / 0.41 (37100) covalent geometry : angle 2.27410 / 1.48 (50537) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 3.63488 / 1.82 ( 2) hydrogen bonds : bond 0.05205 / 3.44 ( 1871) hydrogen bonds : angle 5.10677 / 3.53 ( 5397) metal coordination : bond 0.02624 / 1.66 ( 36) metal coordination : angle 30.77396 / 21.45 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1029 time to evaluate : 1.382 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: 1 53 VAL cc_start: 0.8561 (m) cc_final: 0.8336 (p) REVERT: 1 189 MET cc_start: 0.6606 (mtm) cc_final: 0.6159 (mtm) REVERT: 1 201 LEU cc_start: 0.8241 (mt) cc_final: 0.8020 (mt) REVERT: 1 240 GLN cc_start: 0.5559 (mp10) cc_final: 0.5174 (tm-30) REVERT: 1 241 MET cc_start: 0.6201 (mtt) cc_final: 0.5956 (mtp) REVERT: 1 352 SER cc_start: 0.8858 (t) cc_final: 0.8542 (p) REVERT: 1 367 MET cc_start: 0.8275 (tmm) cc_final: 0.7810 (tmm) REVERT: 2 8 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6999 (mm110) REVERT: 2 9 ASP cc_start: 0.6754 (m-30) cc_final: 0.6173 (t0) REVERT: 2 28 MET cc_start: 0.8216 (mmm) cc_final: 0.7567 (mmm) REVERT: 2 35 GLN cc_start: 0.8480 (tp40) cc_final: 0.7206 (tm-30) REVERT: 2 36 GLN cc_start: 0.8874 (mt0) cc_final: 0.8020 (mt0) REVERT: 2 141 TYR cc_start: 0.7930 (m-80) cc_final: 0.7075 (m-80) REVERT: 3 42 ILE cc_start: 0.9089 (tp) cc_final: 0.8871 (tt) REVERT: 3 47 MET cc_start: 0.8337 (mmm) cc_final: 0.8057 (tpp) REVERT: 3 82 SER cc_start: 0.9329 (m) cc_final: 0.8786 (p) REVERT: 3 136 GLU cc_start: 0.7367 (pt0) cc_final: 0.6801 (pt0) REVERT: 3 228 ASP cc_start: 0.8422 (m-30) cc_final: 0.8170 (t0) REVERT: 3 404 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7755 (mp0) REVERT: 3 459 MET cc_start: 0.8139 (mtt) cc_final: 0.7792 (mtm) REVERT: 3 519 GLU cc_start: 0.7456 (tp30) cc_final: 0.6571 (pp20) REVERT: 3 531 LYS cc_start: 0.7900 (mppt) cc_final: 0.7382 (mmtt) REVERT: 3 533 LEU cc_start: 0.8988 (mt) cc_final: 0.8654 (mt) REVERT: 3 585 MET cc_start: 0.8667 (mmm) cc_final: 0.8328 (mmt) REVERT: 3 655 ARG cc_start: 0.8454 (mpp-170) cc_final: 0.7889 (mtp85) REVERT: 3 772 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7123 (mp0) REVERT: 4 71 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8166 (mt-10) REVERT: 4 138 LEU cc_start: 0.8390 (tp) cc_final: 0.8133 (tp) REVERT: 4 158 ASP cc_start: 0.8897 (m-30) cc_final: 0.8493 (t0) REVERT: 4 170 HIS cc_start: 0.7731 (m-70) cc_final: 0.7501 (m90) REVERT: 4 217 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7620 (mtp180) REVERT: 4 238 SER cc_start: 0.8941 (m) cc_final: 0.8512 (p) REVERT: 4 322 GLU cc_start: 0.8825 (pm20) cc_final: 0.8313 (pt0) REVERT: 4 364 MET cc_start: 0.8939 (mtm) cc_final: 0.8699 (mtm) REVERT: 4 378 LEU cc_start: 0.8703 (tp) cc_final: 0.8385 (tt) REVERT: 5 56 ASP cc_start: 0.8494 (t0) cc_final: 0.8114 (t0) REVERT: 5 62 ASP cc_start: 0.9016 (m-30) cc_final: 0.8749 (m-30) REVERT: 5 105 THR cc_start: 0.9192 (p) cc_final: 0.8940 (p) REVERT: 5 106 ASP cc_start: 0.8257 (m-30) cc_final: 0.7722 (p0) REVERT: 5 122 PHE cc_start: 0.8092 (m-80) cc_final: 0.7565 (m-80) REVERT: 5 177 LYS cc_start: 0.8185 (tttm) cc_final: 0.7950 (tptm) REVERT: 6 25 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7998 (mt-10) REVERT: 6 27 LEU cc_start: 0.9092 (tp) cc_final: 0.8740 (tp) REVERT: 6 51 MET cc_start: 0.7877 (mmt) cc_final: 0.7612 (tpp) REVERT: 6 86 LYS cc_start: 0.8866 (tptt) cc_final: 0.8524 (tttt) REVERT: 6 92 MET cc_start: 0.8689 (tpp) cc_final: 0.7908 (tpp) REVERT: 6 103 LYS cc_start: 0.8722 (pttt) cc_final: 0.8444 (pttm) REVERT: 6 117 MET cc_start: 0.8851 (ptt) cc_final: 0.8635 (ptp) REVERT: 6 152 MET cc_start: 0.8780 (mtp) cc_final: 0.8576 (mtm) REVERT: 6 157 LYS cc_start: 0.9551 (ttmm) cc_final: 0.9286 (ttmm) REVERT: 9 17 LEU cc_start: 0.9270 (tp) cc_final: 0.9067 (tt) REVERT: 9 44 THR cc_start: 0.8977 (p) cc_final: 0.8555 (t) REVERT: 9 103 LEU cc_start: 0.8917 (mt) cc_final: 0.8328 (tt) REVERT: 9 105 GLU cc_start: 0.8972 (tt0) cc_final: 0.8256 (tp30) REVERT: 9 149 GLU cc_start: 0.7870 (tt0) cc_final: 0.7494 (mm-30) REVERT: 7 86 LEU cc_start: 0.8360 (mp) cc_final: 0.8153 (mp) REVERT: 7 90 HIS cc_start: 0.7409 (p90) cc_final: 0.6342 (t70) REVERT: 7 104 VAL cc_start: 0.8083 (m) cc_final: 0.7853 (p) REVERT: A 56 ARG cc_start: 0.8274 (tpp-160) cc_final: 0.7636 (ptt180) REVERT: A 66 MET cc_start: 0.7945 (tmm) cc_final: 0.7601 (tmm) REVERT: A 72 ASP cc_start: 0.8595 (t70) cc_final: 0.8391 (t70) REVERT: L 25 ARG cc_start: 0.7182 (mtm180) cc_final: 0.5629 (mmt180) REVERT: L 75 PHE cc_start: 0.7317 (t80) cc_final: 0.6587 (t80) REVERT: L 101 TYR cc_start: 0.7498 (p90) cc_final: 0.7260 (p90) REVERT: L 114 MET cc_start: 0.7526 (mmm) cc_final: 0.7151 (tpt) REVERT: L 128 PHE cc_start: 0.7979 (t80) cc_final: 0.7771 (t80) REVERT: L 131 TRP cc_start: 0.7412 (m-10) cc_final: 0.7108 (m100) REVERT: L 204 LEU cc_start: 0.9108 (tp) cc_final: 0.8888 (tp) REVERT: L 214 VAL cc_start: 0.8794 (t) cc_final: 0.8554 (t) REVERT: L 225 TRP cc_start: 0.8176 (p-90) cc_final: 0.7664 (p-90) REVERT: L 265 ASP cc_start: 0.7958 (p0) cc_final: 0.6895 (t70) REVERT: L 283 LEU cc_start: 0.8694 (tp) cc_final: 0.8406 (tp) REVERT: L 334 LEU cc_start: 0.8644 (mp) cc_final: 0.8250 (mp) REVERT: L 349 VAL cc_start: 0.7849 (t) cc_final: 0.7538 (t) REVERT: L 377 PRO cc_start: 0.6799 (Cg_exo) cc_final: 0.6498 (Cg_endo) REVERT: L 415 MET cc_start: 0.8174 (mmm) cc_final: 0.7851 (mpp) REVERT: L 576 GLN cc_start: 0.8118 (mt0) cc_final: 0.7266 (tm-30) REVERT: M 31 LEU cc_start: 0.8743 (tp) cc_final: 0.8493 (tp) REVERT: M 55 LEU cc_start: 0.8235 (tp) cc_final: 0.8024 (tp) REVERT: M 100 LEU cc_start: 0.9064 (mt) cc_final: 0.8698 (mm) REVERT: M 109 LEU cc_start: 0.9130 (tp) cc_final: 0.8868 (tp) REVERT: M 219 GLN cc_start: 0.8583 (mt0) cc_final: 0.8052 (mt0) REVERT: M 235 LYS cc_start: 0.8779 (mttt) cc_final: 0.8518 (mttm) REVERT: M 281 PHE cc_start: 0.6663 (m-80) cc_final: 0.6439 (m-80) REVERT: M 282 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8144 (mttm) REVERT: M 285 LEU cc_start: 0.8882 (mp) cc_final: 0.8431 (mp) REVERT: M 377 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8109 (mm-30) REVERT: M 391 LEU cc_start: 0.9045 (tp) cc_final: 0.8844 (tt) REVERT: M 443 MET cc_start: 0.8795 (mtt) cc_final: 0.8544 (mtp) REVERT: N 3 LEU cc_start: 0.9008 (tp) cc_final: 0.8758 (tp) REVERT: N 39 SER cc_start: 0.9173 (t) cc_final: 0.8882 (p) REVERT: N 40 LEU cc_start: 0.7918 (tp) cc_final: 0.7668 (tp) REVERT: N 95 MET cc_start: 0.8871 (mtp) cc_final: 0.7948 (ttm) REVERT: N 103 HIS cc_start: 0.7964 (t-90) cc_final: 0.7654 (t-170) REVERT: N 153 LEU cc_start: 0.9162 (mm) cc_final: 0.8828 (mm) REVERT: N 269 MET cc_start: 0.8729 (mtp) cc_final: 0.8217 (ttm) REVERT: N 318 LYS cc_start: 0.8143 (mttm) cc_final: 0.7347 (tptt) REVERT: N 326 PHE cc_start: 0.9167 (t80) cc_final: 0.8407 (t80) REVERT: N 333 LEU cc_start: 0.8938 (mt) cc_final: 0.8667 (mp) REVERT: N 345 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8160 (mmmm) REVERT: N 363 LEU cc_start: 0.7870 (mt) cc_final: 0.7316 (tt) REVERT: H 95 LEU cc_start: 0.8859 (mm) cc_final: 0.8472 (mm) REVERT: H 137 PHE cc_start: 0.8487 (p90) cc_final: 0.7723 (p90) REVERT: H 149 LEU cc_start: 0.8856 (tp) cc_final: 0.8305 (tp) REVERT: H 181 ASN cc_start: 0.7926 (m-40) cc_final: 0.7623 (t0) REVERT: H 195 LEU cc_start: 0.8851 (mt) cc_final: 0.8650 (mt) REVERT: H 246 MET cc_start: 0.7574 (ttm) cc_final: 0.7236 (ttt) REVERT: H 250 ILE cc_start: 0.9250 (tp) cc_final: 0.9023 (tp) REVERT: H 281 LEU cc_start: 0.8076 (mt) cc_final: 0.7857 (mt) outliers start: 7 outliers final: 1 residues processed: 1033 average time/residue: 0.2140 time to fit residues: 372.0488 Evaluate side-chains 751 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 750 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 117 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 324 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 147 GLN ** 2 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 591 HIS 3 703 GLN 4 63 HIS 5 40 HIS 6 155 GLN 7 92 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 GLN ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN N 96 HIS ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103241 restraints weight = 83340.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104291 restraints weight = 56379.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105746 restraints weight = 42631.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106067 restraints weight = 35065.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106275 restraints weight = 29006.580| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 37137 Z= 0.405 Angle : 2.613 55.876 50632 Z= 1.475 Chirality : 0.445 6.472 5672 Planarity : 0.006 0.055 6377 Dihedral : 6.553 172.641 5099 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.96 % Favored : 93.76 % Rotamer: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.59 (0.12), residues: 4612 helix: 0.85 (0.10), residues: 2451 sheet: -0.92 (0.32), residues: 251 loop : -2.03 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 397 TYR 0.032 0.002 TYR H 147 PHE 0.033 0.002 PHE H 244 TRP 0.022 0.001 TRP M 415 HIS 0.011 0.001 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01166 / 0.41 (37100) covalent geometry : angle 2.25753 / 1.47 (50537) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 2.44832 / 1.23 ( 2) hydrogen bonds : bond 0.04772 / 3.16 ( 1871) hydrogen bonds : angle 4.86162 / 3.37 ( 5397) metal coordination : bond 0.02210 / 1.44 ( 36) metal coordination : angle 30.78805 / 21.38 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 978 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 91 CYS cc_start: 0.8915 (t) cc_final: 0.8692 (t) REVERT: 1 102 LYS cc_start: 0.8474 (pttt) cc_final: 0.8256 (pttt) REVERT: 1 118 MET cc_start: 0.7243 (ttm) cc_final: 0.6082 (ttm) REVERT: 1 189 MET cc_start: 0.6574 (mtm) cc_final: 0.6187 (mtm) REVERT: 1 268 MET cc_start: 0.6700 (ttm) cc_final: 0.6286 (ttm) REVERT: 1 270 THR cc_start: 0.8756 (p) cc_final: 0.8361 (t) REVERT: 1 352 SER cc_start: 0.8782 (t) cc_final: 0.8410 (p) REVERT: 1 367 MET cc_start: 0.8289 (tmm) cc_final: 0.7782 (tmm) REVERT: 2 8 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7147 (mm110) REVERT: 2 9 ASP cc_start: 0.6783 (m-30) cc_final: 0.6213 (t0) REVERT: 2 28 MET cc_start: 0.8244 (mmm) cc_final: 0.7727 (mmm) REVERT: 2 35 GLN cc_start: 0.7896 (tp40) cc_final: 0.7317 (tm-30) REVERT: 2 36 GLN cc_start: 0.8996 (mt0) cc_final: 0.8371 (mt0) REVERT: 2 141 TYR cc_start: 0.7500 (m-80) cc_final: 0.7201 (m-80) REVERT: 3 47 MET cc_start: 0.8218 (mmm) cc_final: 0.7866 (tpp) REVERT: 3 78 LYS cc_start: 0.9026 (mttt) cc_final: 0.8826 (mtpp) REVERT: 3 353 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8199 (mm-30) REVERT: 3 459 MET cc_start: 0.8097 (mtt) cc_final: 0.7762 (mtm) REVERT: 3 519 GLU cc_start: 0.7360 (tp30) cc_final: 0.6508 (pp20) REVERT: 3 531 LYS cc_start: 0.7789 (mppt) cc_final: 0.7259 (mmtt) REVERT: 3 533 LEU cc_start: 0.9026 (mt) cc_final: 0.8699 (mt) REVERT: 3 585 MET cc_start: 0.8507 (mmm) cc_final: 0.8035 (mmm) REVERT: 3 655 ARG cc_start: 0.8485 (mpp-170) cc_final: 0.7954 (mtp85) REVERT: 3 772 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7094 (mp0) REVERT: 4 138 LEU cc_start: 0.8483 (tp) cc_final: 0.8135 (tp) REVERT: 4 274 ASP cc_start: 0.7740 (m-30) cc_final: 0.6982 (m-30) REVERT: 4 322 GLU cc_start: 0.8948 (pm20) cc_final: 0.8382 (pt0) REVERT: 4 364 MET cc_start: 0.8912 (mtm) cc_final: 0.8554 (mtm) REVERT: 5 62 ASP cc_start: 0.9049 (m-30) cc_final: 0.8780 (m-30) REVERT: 5 106 ASP cc_start: 0.8376 (m-30) cc_final: 0.7905 (p0) REVERT: 5 113 PHE cc_start: 0.7490 (m-10) cc_final: 0.6847 (m-80) REVERT: 5 122 PHE cc_start: 0.8189 (m-80) cc_final: 0.7648 (m-80) REVERT: 5 170 PHE cc_start: 0.8036 (m-10) cc_final: 0.7685 (m-10) REVERT: 5 177 LYS cc_start: 0.8089 (tttm) cc_final: 0.7837 (tppt) REVERT: 6 25 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8206 (mt-10) REVERT: 6 27 LEU cc_start: 0.8961 (tp) cc_final: 0.8576 (tp) REVERT: 6 86 LYS cc_start: 0.8797 (tptt) cc_final: 0.8478 (tttt) REVERT: 6 92 MET cc_start: 0.8417 (tpp) cc_final: 0.8099 (tpp) REVERT: 6 108 MET cc_start: 0.9030 (ttt) cc_final: 0.8752 (ttt) REVERT: 6 126 ASN cc_start: 0.8514 (t0) cc_final: 0.8287 (t0) REVERT: 9 3 LEU cc_start: 0.9198 (mt) cc_final: 0.8944 (mt) REVERT: 9 17 LEU cc_start: 0.9125 (tp) cc_final: 0.8891 (tt) REVERT: 9 44 THR cc_start: 0.9012 (p) cc_final: 0.8592 (t) REVERT: 9 79 ASN cc_start: 0.7949 (m-40) cc_final: 0.6920 (m110) REVERT: 9 91 TYR cc_start: 0.9303 (t80) cc_final: 0.7758 (t80) REVERT: 9 93 ILE cc_start: 0.9398 (mt) cc_final: 0.9159 (mt) REVERT: 9 103 LEU cc_start: 0.9076 (mt) cc_final: 0.8338 (tt) REVERT: 9 105 GLU cc_start: 0.8915 (tt0) cc_final: 0.8322 (tt0) REVERT: 9 121 MET cc_start: 0.8655 (ptp) cc_final: 0.8286 (ptp) REVERT: 9 149 GLU cc_start: 0.7979 (tt0) cc_final: 0.7504 (mm-30) REVERT: 7 86 LEU cc_start: 0.8340 (mp) cc_final: 0.8100 (mp) REVERT: 7 90 HIS cc_start: 0.7417 (p90) cc_final: 0.6378 (t70) REVERT: 7 104 VAL cc_start: 0.8166 (m) cc_final: 0.7927 (p) REVERT: A 56 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.7611 (ptt180) REVERT: A 66 MET cc_start: 0.8214 (tmm) cc_final: 0.7841 (tmm) REVERT: A 67 LEU cc_start: 0.8913 (tp) cc_final: 0.8436 (tt) REVERT: A 97 LEU cc_start: 0.8934 (tp) cc_final: 0.8723 (tt) REVERT: A 99 PHE cc_start: 0.9253 (t80) cc_final: 0.8961 (t80) REVERT: A 103 LEU cc_start: 0.9492 (mm) cc_final: 0.9116 (mm) REVERT: J 144 PHE cc_start: 0.8544 (t80) cc_final: 0.8296 (t80) REVERT: K 36 ASN cc_start: 0.7676 (m-40) cc_final: 0.6579 (m110) REVERT: L 25 ARG cc_start: 0.5523 (mtm180) cc_final: 0.5106 (mmt180) REVERT: L 75 PHE cc_start: 0.7070 (t80) cc_final: 0.6505 (t80) REVERT: L 101 TYR cc_start: 0.7501 (p90) cc_final: 0.7270 (p90) REVERT: L 114 MET cc_start: 0.7581 (mmm) cc_final: 0.7172 (tpt) REVERT: L 131 TRP cc_start: 0.7633 (m-10) cc_final: 0.7389 (m100) REVERT: L 148 ASN cc_start: 0.7644 (m110) cc_final: 0.7271 (m110) REVERT: L 214 VAL cc_start: 0.8777 (t) cc_final: 0.8282 (t) REVERT: L 225 TRP cc_start: 0.8296 (p-90) cc_final: 0.7798 (p-90) REVERT: L 265 ASP cc_start: 0.7989 (p0) cc_final: 0.6956 (t70) REVERT: L 283 LEU cc_start: 0.8712 (tp) cc_final: 0.8439 (tp) REVERT: L 316 TRP cc_start: 0.7220 (p-90) cc_final: 0.7007 (p-90) REVERT: L 334 LEU cc_start: 0.8500 (mp) cc_final: 0.8157 (mp) REVERT: L 415 MET cc_start: 0.7937 (mmm) cc_final: 0.7653 (mmm) REVERT: L 416 TYR cc_start: 0.8666 (p90) cc_final: 0.8288 (p90) REVERT: L 442 MET cc_start: 0.6887 (mtt) cc_final: 0.5371 (mtp) REVERT: L 479 GLU cc_start: 0.6290 (pt0) cc_final: 0.5990 (tt0) REVERT: L 576 GLN cc_start: 0.8055 (mt0) cc_final: 0.7355 (tm-30) REVERT: L 581 LEU cc_start: 0.7491 (pp) cc_final: 0.7111 (tt) REVERT: M 3 VAL cc_start: 0.8618 (t) cc_final: 0.8276 (p) REVERT: M 68 ASP cc_start: 0.8410 (m-30) cc_final: 0.8202 (m-30) REVERT: M 122 PHE cc_start: 0.8408 (t80) cc_final: 0.8057 (t80) REVERT: M 150 LEU cc_start: 0.7582 (tp) cc_final: 0.7350 (tp) REVERT: M 203 ILE cc_start: 0.8161 (tt) cc_final: 0.7882 (tt) REVERT: M 219 GLN cc_start: 0.8770 (mt0) cc_final: 0.8325 (mt0) REVERT: M 221 ASN cc_start: 0.8584 (t0) cc_final: 0.8334 (t0) REVERT: M 282 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8271 (mttm) REVERT: M 285 LEU cc_start: 0.9149 (mp) cc_final: 0.8833 (mp) REVERT: M 325 LEU cc_start: 0.8759 (tp) cc_final: 0.8394 (tp) REVERT: M 339 LEU cc_start: 0.6835 (tp) cc_final: 0.6618 (tp) REVERT: M 410 PHE cc_start: 0.8467 (t80) cc_final: 0.8196 (t80) REVERT: M 412 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8338 (ttmt) REVERT: N 3 LEU cc_start: 0.8978 (tp) cc_final: 0.8647 (tp) REVERT: N 40 LEU cc_start: 0.8070 (tp) cc_final: 0.7765 (tp) REVERT: N 103 HIS cc_start: 0.7996 (t-90) cc_final: 0.7447 (t-170) REVERT: N 153 LEU cc_start: 0.9170 (mm) cc_final: 0.8924 (mm) REVERT: N 171 LEU cc_start: 0.9188 (tp) cc_final: 0.8872 (tp) REVERT: N 208 VAL cc_start: 0.9281 (t) cc_final: 0.8995 (t) REVERT: N 211 MET cc_start: 0.7357 (mtm) cc_final: 0.6836 (mtm) REVERT: N 318 LYS cc_start: 0.8159 (mttm) cc_final: 0.7314 (tptt) REVERT: N 326 PHE cc_start: 0.9154 (t80) cc_final: 0.8397 (t80) REVERT: N 330 MET cc_start: 0.8681 (mmp) cc_final: 0.8383 (mmp) REVERT: N 333 LEU cc_start: 0.8927 (mt) cc_final: 0.8692 (tp) REVERT: N 363 LEU cc_start: 0.8167 (mt) cc_final: 0.7415 (tt) REVERT: N 387 GLU cc_start: 0.7928 (tp30) cc_final: 0.7212 (tm-30) REVERT: H 137 PHE cc_start: 0.8569 (p90) cc_final: 0.7692 (p90) REVERT: H 149 LEU cc_start: 0.8857 (tp) cc_final: 0.8507 (tp) REVERT: H 181 ASN cc_start: 0.7882 (m-40) cc_final: 0.7545 (t0) REVERT: H 196 PHE cc_start: 0.7493 (p90) cc_final: 0.7182 (p90) REVERT: H 264 LEU cc_start: 0.8647 (mt) cc_final: 0.8175 (mp) outliers start: 1 outliers final: 0 residues processed: 979 average time/residue: 0.2140 time to fit residues: 355.6522 Evaluate side-chains 761 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 761 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 296 optimal weight: 8.9990 chunk 409 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 35 HIS ** 2 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 114 ASN 3 347 HIS ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 465 HIS 3 657 HIS 6 155 GLN 7 92 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 341 HIS L 432 HIS L 434 HIS M 186 GLN M 211 HIS N 60 GLN ** N 201 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 = 0.3428 r_free = 0.3428 target = 0.112148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099146 restraints weight = 83049.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100041 restraints weight = 59556.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100789 restraints weight = 49102.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101201 restraints weight = 41834.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101467 restraints weight = 35405.512| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.252 37137 Z= 0.435 Angle : 2.673 74.427 50632 Z= 1.489 Chirality : 0.444 6.508 5672 Planarity : 0.006 0.065 6377 Dihedral : 6.710 174.347 5099 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.70 % Favored : 93.04 % Rotamer: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % 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: -0.77 (0.12), residues: 4612 helix: 0.66 (0.10), residues: 2456 sheet: -1.09 (0.28), residues: 313 loop : -2.04 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 37 TYR 0.039 0.002 TYR H 147 PHE 0.048 0.003 PHE 4 150 TRP 0.023 0.002 TRP 6 96 HIS 0.010 0.002 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.43 (37100) covalent geometry : angle 2.28943 / 1.49 (50537) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 1.95238 / 0.99 ( 2) hydrogen bonds : bond 0.05144 / 3.40 ( 1871) hydrogen bonds : angle 5.05740 / 3.51 ( 5397) metal coordination : bond 0.02431 / 1.47 ( 36) metal coordination : angle 32.29078 / 22.69 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 912 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 102 LYS cc_start: 0.8579 (pttt) cc_final: 0.8219 (pttt) REVERT: 1 185 GLU cc_start: 0.8051 (pm20) cc_final: 0.7341 (pt0) REVERT: 1 189 MET cc_start: 0.6665 (mtm) cc_final: 0.6147 (mtm) REVERT: 1 268 MET cc_start: 0.6583 (ttm) cc_final: 0.6253 (ttm) REVERT: 1 270 THR cc_start: 0.8820 (p) cc_final: 0.8358 (t) REVERT: 1 352 SER cc_start: 0.8708 (t) cc_final: 0.8422 (p) REVERT: 1 367 MET cc_start: 0.8392 (tmm) cc_final: 0.7937 (tmm) REVERT: 2 9 ASP cc_start: 0.6816 (m-30) cc_final: 0.6326 (t0) REVERT: 2 28 MET cc_start: 0.8087 (mmm) cc_final: 0.7450 (mmm) REVERT: 2 35 GLN cc_start: 0.8224 (tp40) cc_final: 0.7304 (tm-30) REVERT: 2 36 GLN cc_start: 0.8900 (mt0) cc_final: 0.8138 (mt0) REVERT: 2 77 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7876 (mmtt) REVERT: 3 36 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8537 (tm-30) REVERT: 3 47 MET cc_start: 0.8494 (mmm) cc_final: 0.8205 (tpp) REVERT: 3 177 ASP cc_start: 0.6509 (m-30) cc_final: 0.6307 (m-30) REVERT: 3 382 PHE cc_start: 0.7050 (m-10) cc_final: 0.6825 (m-10) REVERT: 3 459 MET cc_start: 0.8148 (mtt) cc_final: 0.7775 (mtm) REVERT: 3 519 GLU cc_start: 0.7279 (tp30) cc_final: 0.6212 (pp20) REVERT: 3 531 LYS cc_start: 0.7609 (mppt) cc_final: 0.6840 (mmtt) REVERT: 3 533 LEU cc_start: 0.8871 (mt) cc_final: 0.8588 (mt) REVERT: 3 585 MET cc_start: 0.8463 (mmm) cc_final: 0.8088 (mmm) REVERT: 3 655 ARG cc_start: 0.8754 (mpp-170) cc_final: 0.8019 (mtp85) REVERT: 3 746 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.7110 (ttm170) REVERT: 4 138 LEU cc_start: 0.8854 (tp) cc_final: 0.8508 (tp) REVERT: 4 238 SER cc_start: 0.9046 (m) cc_final: 0.8659 (p) REVERT: 4 274 ASP cc_start: 0.8172 (m-30) cc_final: 0.7463 (m-30) REVERT: 4 364 MET cc_start: 0.8835 (mtm) cc_final: 0.8582 (mtm) REVERT: 5 73 GLU cc_start: 0.7754 (tt0) cc_final: 0.7419 (tm-30) REVERT: 5 100 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7391 (mmm-85) REVERT: 5 106 ASP cc_start: 0.8185 (m-30) cc_final: 0.7892 (p0) REVERT: 5 113 PHE cc_start: 0.7964 (m-10) cc_final: 0.7202 (m-80) REVERT: 5 122 PHE cc_start: 0.8122 (m-80) cc_final: 0.7723 (m-80) REVERT: 5 177 LYS cc_start: 0.8235 (tttm) cc_final: 0.7962 (tppt) REVERT: 6 25 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8040 (mt-10) REVERT: 6 27 LEU cc_start: 0.9124 (tp) cc_final: 0.8788 (tp) REVERT: 6 86 LYS cc_start: 0.8857 (tptt) cc_final: 0.8498 (tttt) REVERT: 6 92 MET cc_start: 0.8484 (tpp) cc_final: 0.8080 (tpp) REVERT: 6 94 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8026 (tmm-80) REVERT: 9 103 LEU cc_start: 0.9108 (mt) cc_final: 0.8590 (tt) REVERT: 9 105 GLU cc_start: 0.8840 (tt0) cc_final: 0.8398 (tt0) REVERT: 9 121 MET cc_start: 0.8663 (ptp) cc_final: 0.8180 (ptm) REVERT: 9 126 TYR cc_start: 0.7864 (t80) cc_final: 0.7452 (t80) REVERT: 7 21 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7648 (mtt180) REVERT: 7 39 ASP cc_start: 0.9266 (p0) cc_final: 0.9005 (p0) REVERT: 7 86 LEU cc_start: 0.8454 (mp) cc_final: 0.8198 (mp) REVERT: 7 90 HIS cc_start: 0.7414 (p90) cc_final: 0.6492 (t70) REVERT: A 56 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.7588 (ptt180) REVERT: A 66 MET cc_start: 0.8190 (tmm) cc_final: 0.7932 (tmm) REVERT: A 67 LEU cc_start: 0.9012 (tp) cc_final: 0.8628 (tt) REVERT: A 71 PHE cc_start: 0.8153 (m-10) cc_final: 0.7738 (m-80) REVERT: A 72 ASP cc_start: 0.8214 (t70) cc_final: 0.7991 (t70) REVERT: J 36 PHE cc_start: 0.8051 (m-10) cc_final: 0.7834 (m-10) REVERT: J 132 TYR cc_start: 0.8602 (m-80) cc_final: 0.8302 (m-10) REVERT: K 36 ASN cc_start: 0.7637 (m-40) cc_final: 0.7359 (m-40) REVERT: L 25 ARG cc_start: 0.5809 (mtm180) cc_final: 0.5111 (mmt180) REVERT: L 28 LEU cc_start: 0.7635 (tp) cc_final: 0.7289 (tp) REVERT: L 75 PHE cc_start: 0.7355 (t80) cc_final: 0.6902 (t80) REVERT: L 101 TYR cc_start: 0.7594 (p90) cc_final: 0.7344 (p90) REVERT: L 148 ASN cc_start: 0.7609 (m110) cc_final: 0.7170 (m110) REVERT: L 222 LEU cc_start: 0.8780 (pp) cc_final: 0.8443 (pp) REVERT: L 225 TRP cc_start: 0.8545 (p-90) cc_final: 0.8117 (p-90) REVERT: L 265 ASP cc_start: 0.7926 (p0) cc_final: 0.6918 (t70) REVERT: L 316 TRP cc_start: 0.7369 (p-90) cc_final: 0.6984 (p-90) REVERT: L 331 LEU cc_start: 0.8435 (tp) cc_final: 0.8214 (tp) REVERT: L 334 LEU cc_start: 0.8424 (mp) cc_final: 0.7758 (mp) REVERT: L 415 MET cc_start: 0.7918 (mmm) cc_final: 0.7695 (mpp) REVERT: L 416 TYR cc_start: 0.8851 (p90) cc_final: 0.8481 (p90) REVERT: L 442 MET cc_start: 0.7763 (mtt) cc_final: 0.6186 (mtp) REVERT: L 576 GLN cc_start: 0.7928 (mt0) cc_final: 0.7364 (tm-30) REVERT: L 581 LEU cc_start: 0.7378 (pp) cc_final: 0.7060 (tt) REVERT: M 16 LEU cc_start: 0.8820 (mt) cc_final: 0.8536 (tp) REVERT: M 100 LEU cc_start: 0.9139 (mm) cc_final: 0.8880 (mm) REVERT: M 103 GLU cc_start: 0.8379 (tt0) cc_final: 0.8047 (tp30) REVERT: M 122 PHE cc_start: 0.8431 (t80) cc_final: 0.8208 (t80) REVERT: M 150 LEU cc_start: 0.7946 (tp) cc_final: 0.7706 (tp) REVERT: M 221 ASN cc_start: 0.8691 (t0) cc_final: 0.8467 (t0) REVERT: M 282 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8217 (mttm) REVERT: M 293 MET cc_start: 0.8368 (mmp) cc_final: 0.8039 (mpp) REVERT: M 432 PHE cc_start: 0.7850 (t80) cc_final: 0.7554 (t80) REVERT: N 1 MET cc_start: 0.7565 (mmp) cc_final: 0.7141 (mmp) REVERT: N 95 MET cc_start: 0.8737 (mtp) cc_final: 0.8070 (ttm) REVERT: N 103 HIS cc_start: 0.8266 (t-90) cc_final: 0.7666 (t-170) REVERT: N 207 VAL cc_start: 0.8513 (t) cc_final: 0.8101 (m) REVERT: N 268 TYR cc_start: 0.7794 (m-80) cc_final: 0.7506 (m-80) REVERT: N 318 LYS cc_start: 0.8197 (mttm) cc_final: 0.7314 (tptt) REVERT: N 326 PHE cc_start: 0.9276 (t80) cc_final: 0.8550 (t80) REVERT: N 333 LEU cc_start: 0.9116 (mt) cc_final: 0.8893 (tp) REVERT: N 345 LYS cc_start: 0.8251 (mmmm) cc_final: 0.8015 (mmmm) REVERT: N 363 LEU cc_start: 0.8526 (mt) cc_final: 0.7698 (tt) REVERT: N 387 GLU cc_start: 0.7918 (tp30) cc_final: 0.7516 (tm-30) REVERT: H 35 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7363 (tm-30) REVERT: H 95 LEU cc_start: 0.8809 (mm) cc_final: 0.8537 (mm) REVERT: H 130 GLU cc_start: 0.7867 (tp30) cc_final: 0.7553 (tp30) REVERT: H 137 PHE cc_start: 0.8644 (p90) cc_final: 0.7995 (p90) REVERT: H 149 LEU cc_start: 0.8839 (tp) cc_final: 0.8595 (tp) REVERT: H 163 GLU cc_start: 0.6261 (tp30) cc_final: 0.5797 (tp30) REVERT: H 181 ASN cc_start: 0.7869 (m-40) cc_final: 0.7380 (t0) REVERT: H 196 PHE cc_start: 0.7364 (p90) cc_final: 0.7154 (p90) REVERT: H 281 LEU cc_start: 0.8432 (mt) cc_final: 0.8140 (mt) outliers start: 1 outliers final: 0 residues processed: 913 average time/residue: 0.2147 time to fit residues: 331.1833 Evaluate side-chains 700 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 426 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 404 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 456 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 425 optimal weight: 1.9990 chunk 442 optimal weight: 0.7980 chunk 51 optimal weight: 30.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 87 HIS 1 147 GLN 1 208 GLN ** 2 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 58 ASN ** 6 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 155 GLN ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101074 restraints weight = 82813.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101755 restraints weight = 62611.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102358 restraints weight = 50947.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102730 restraints weight = 44290.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103003 restraints weight = 37614.122| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.253 37137 Z= 0.410 Angle : 2.638 67.874 50632 Z= 1.478 Chirality : 0.443 6.435 5672 Planarity : 0.005 0.083 6377 Dihedral : 6.489 176.652 5099 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.11 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.55 (0.12), residues: 4612 helix: 0.85 (0.10), residues: 2453 sheet: -1.03 (0.30), residues: 291 loop : -1.94 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 522 TYR 0.032 0.002 TYR H 147 PHE 0.031 0.002 PHE 4 150 TRP 0.030 0.001 TRP L 131 HIS 0.012 0.001 HIS 4 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01175 / 0.41 (37100) covalent geometry : angle 2.26511 / 1.47 (50537) SS BOND : bond 0.01036 / 0.55 ( 1) SS BOND : angle 3.49817 / 1.97 ( 2) hydrogen bonds : bond 0.04687 / 3.11 ( 1871) hydrogen bonds : angle 4.85671 / 3.37 ( 5397) metal coordination : bond 0.02056 / 1.30 ( 36) metal coordination : angle 31.64453 / 22.22 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 923 time to evaluate : 1.385 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: 1 91 CYS cc_start: 0.8547 (t) cc_final: 0.8324 (t) REVERT: 1 102 LYS cc_start: 0.8382 (pttt) cc_final: 0.7992 (pttt) REVERT: 1 189 MET cc_start: 0.6379 (mtm) cc_final: 0.6068 (mtm) REVERT: 1 201 LEU cc_start: 0.8392 (mt) cc_final: 0.8175 (mt) REVERT: 1 268 MET cc_start: 0.7377 (ttm) cc_final: 0.7124 (ttm) REVERT: 1 270 THR cc_start: 0.8909 (p) cc_final: 0.8415 (t) REVERT: 1 352 SER cc_start: 0.8614 (t) cc_final: 0.8330 (p) REVERT: 1 367 MET cc_start: 0.8209 (tmm) cc_final: 0.7930 (tmm) REVERT: 2 9 ASP cc_start: 0.6734 (m-30) cc_final: 0.6309 (t0) REVERT: 2 28 MET cc_start: 0.8209 (mmm) cc_final: 0.7835 (mmt) REVERT: 2 35 GLN cc_start: 0.8048 (tp40) cc_final: 0.7452 (tm-30) REVERT: 2 36 GLN cc_start: 0.8910 (mt0) cc_final: 0.8107 (mt0) REVERT: 2 141 TYR cc_start: 0.7528 (m-80) cc_final: 0.6889 (m-80) REVERT: 3 36 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8503 (tm-30) REVERT: 3 47 MET cc_start: 0.8181 (mmm) cc_final: 0.7919 (tpp) REVERT: 3 275 LEU cc_start: 0.9119 (mm) cc_final: 0.8768 (mt) REVERT: 3 331 GLU cc_start: 0.7607 (tm-30) cc_final: 0.6932 (tm-30) REVERT: 3 353 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8434 (mm-30) REVERT: 3 459 MET cc_start: 0.8120 (mtt) cc_final: 0.7737 (mtm) REVERT: 3 519 GLU cc_start: 0.7260 (tp30) cc_final: 0.6293 (pp20) REVERT: 3 531 LYS cc_start: 0.7357 (mppt) cc_final: 0.6739 (mmtt) REVERT: 3 533 LEU cc_start: 0.8970 (mt) cc_final: 0.8581 (mt) REVERT: 3 655 ARG cc_start: 0.8674 (mpp-170) cc_final: 0.7923 (mtp85) REVERT: 4 67 GLU cc_start: 0.8482 (pm20) cc_final: 0.8242 (pm20) REVERT: 4 138 LEU cc_start: 0.8836 (tp) cc_final: 0.8463 (tp) REVERT: 4 238 SER cc_start: 0.8989 (m) cc_final: 0.8591 (p) REVERT: 4 271 ASP cc_start: 0.7197 (m-30) cc_final: 0.6741 (m-30) REVERT: 4 274 ASP cc_start: 0.8215 (m-30) cc_final: 0.7743 (m-30) REVERT: 4 364 MET cc_start: 0.8823 (mtm) cc_final: 0.8543 (mtm) REVERT: 5 73 GLU cc_start: 0.7761 (tt0) cc_final: 0.7362 (tm-30) REVERT: 5 106 ASP cc_start: 0.8178 (m-30) cc_final: 0.7966 (p0) REVERT: 5 122 PHE cc_start: 0.8125 (m-80) cc_final: 0.7735 (m-80) REVERT: 5 170 PHE cc_start: 0.7636 (m-10) cc_final: 0.7211 (m-10) REVERT: 5 177 LYS cc_start: 0.8289 (tttm) cc_final: 0.7928 (tppt) REVERT: 6 25 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8051 (mt-10) REVERT: 6 27 LEU cc_start: 0.8856 (tp) cc_final: 0.8438 (tp) REVERT: 6 63 PHE cc_start: 0.8016 (m-80) cc_final: 0.7641 (m-80) REVERT: 6 86 LYS cc_start: 0.8837 (tptt) cc_final: 0.8569 (tttt) REVERT: 6 92 MET cc_start: 0.8606 (tpp) cc_final: 0.8062 (tpp) REVERT: 6 126 ASN cc_start: 0.8623 (t0) cc_final: 0.8331 (t0) REVERT: 6 133 VAL cc_start: 0.9024 (t) cc_final: 0.8794 (t) REVERT: 6 157 LYS cc_start: 0.9494 (ttmm) cc_final: 0.9113 (ttmm) REVERT: 9 3 LEU cc_start: 0.8962 (mt) cc_final: 0.8403 (tp) REVERT: 9 17 LEU cc_start: 0.9254 (tp) cc_final: 0.9045 (tt) REVERT: 9 44 THR cc_start: 0.9061 (p) cc_final: 0.8668 (t) REVERT: 9 91 TYR cc_start: 0.9257 (t80) cc_final: 0.7806 (t80) REVERT: 9 93 ILE cc_start: 0.9479 (mt) cc_final: 0.9274 (mt) REVERT: 9 103 LEU cc_start: 0.9154 (mt) cc_final: 0.8394 (tt) REVERT: 9 105 GLU cc_start: 0.8856 (tt0) cc_final: 0.8322 (tt0) REVERT: 9 121 MET cc_start: 0.8720 (ptp) cc_final: 0.8332 (ptp) REVERT: 9 126 TYR cc_start: 0.7974 (t80) cc_final: 0.7417 (t80) REVERT: 7 86 LEU cc_start: 0.8378 (mp) cc_final: 0.8158 (mp) REVERT: 7 90 HIS cc_start: 0.7364 (p90) cc_final: 0.6457 (t70) REVERT: A 56 ARG cc_start: 0.8196 (tpp-160) cc_final: 0.7580 (ptt180) REVERT: A 66 MET cc_start: 0.8225 (tmm) cc_final: 0.7679 (tmm) REVERT: A 67 LEU cc_start: 0.9281 (tp) cc_final: 0.8785 (tt) REVERT: J 36 PHE cc_start: 0.7958 (m-10) cc_final: 0.7632 (m-10) REVERT: J 59 TYR cc_start: 0.8139 (m-10) cc_final: 0.7727 (m-10) REVERT: K 41 SER cc_start: 0.8724 (p) cc_final: 0.8501 (p) REVERT: L 8 LEU cc_start: 0.8487 (mt) cc_final: 0.7903 (pp) REVERT: L 75 PHE cc_start: 0.7277 (t80) cc_final: 0.6816 (t80) REVERT: L 114 MET cc_start: 0.8580 (tpt) cc_final: 0.7184 (tpt) REVERT: L 128 PHE cc_start: 0.8070 (t80) cc_final: 0.7656 (t80) REVERT: L 129 ILE cc_start: 0.8082 (mt) cc_final: 0.7736 (mt) REVERT: L 148 ASN cc_start: 0.7546 (m110) cc_final: 0.6918 (m110) REVERT: L 153 ASP cc_start: 0.7952 (m-30) cc_final: 0.7112 (t0) REVERT: L 170 MET cc_start: 0.8459 (mtm) cc_final: 0.7978 (mtm) REVERT: L 214 VAL cc_start: 0.8900 (t) cc_final: 0.8601 (p) REVERT: L 222 LEU cc_start: 0.8532 (pp) cc_final: 0.8299 (pp) REVERT: L 225 TRP cc_start: 0.8452 (p-90) cc_final: 0.8107 (p-90) REVERT: L 265 ASP cc_start: 0.7852 (p0) cc_final: 0.6937 (t70) REVERT: L 415 MET cc_start: 0.7847 (mmm) cc_final: 0.7641 (mmm) REVERT: L 442 MET cc_start: 0.7753 (mtt) cc_final: 0.6058 (mtp) REVERT: L 558 ARG cc_start: 0.7037 (mmm160) cc_final: 0.6727 (tmt170) REVERT: L 576 GLN cc_start: 0.8022 (mt0) cc_final: 0.7414 (tm-30) REVERT: L 581 LEU cc_start: 0.7184 (pp) cc_final: 0.6977 (tt) REVERT: M 3 VAL cc_start: 0.8526 (t) cc_final: 0.8174 (p) REVERT: M 16 LEU cc_start: 0.8866 (mt) cc_final: 0.8632 (tp) REVERT: M 122 PHE cc_start: 0.8411 (t80) cc_final: 0.8102 (t80) REVERT: M 145 LEU cc_start: 0.8602 (tp) cc_final: 0.8394 (tt) REVERT: M 208 PHE cc_start: 0.7898 (t80) cc_final: 0.7526 (t80) REVERT: M 219 GLN cc_start: 0.8633 (mt0) cc_final: 0.8424 (mt0) REVERT: M 221 ASN cc_start: 0.8778 (t0) cc_final: 0.8500 (t0) REVERT: M 282 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8005 (mttm) REVERT: M 396 PHE cc_start: 0.8136 (m-80) cc_final: 0.7558 (m-80) REVERT: M 410 PHE cc_start: 0.8401 (t80) cc_final: 0.7618 (t80) REVERT: M 412 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8259 (mtmt) REVERT: M 432 PHE cc_start: 0.7701 (t80) cc_final: 0.7435 (t80) REVERT: M 443 MET cc_start: 0.8960 (mtp) cc_final: 0.8348 (mtp) REVERT: N 1 MET cc_start: 0.7330 (mmp) cc_final: 0.6963 (mmp) REVERT: N 95 MET cc_start: 0.8803 (mtp) cc_final: 0.7965 (ttm) REVERT: N 103 HIS cc_start: 0.8273 (t-90) cc_final: 0.7670 (t-170) REVERT: N 136 TYR cc_start: 0.8752 (t80) cc_final: 0.8537 (t80) REVERT: N 153 LEU cc_start: 0.9064 (mm) cc_final: 0.8839 (mm) REVERT: N 171 LEU cc_start: 0.9160 (tp) cc_final: 0.8868 (tp) REVERT: N 211 MET cc_start: 0.6953 (mtm) cc_final: 0.6476 (mtm) REVERT: N 268 TYR cc_start: 0.7688 (m-80) cc_final: 0.7367 (m-80) REVERT: N 326 PHE cc_start: 0.9248 (t80) cc_final: 0.8532 (t80) REVERT: N 333 LEU cc_start: 0.8837 (mt) cc_final: 0.8533 (tp) REVERT: N 363 LEU cc_start: 0.8666 (mt) cc_final: 0.7708 (tt) REVERT: N 387 GLU cc_start: 0.8315 (tp30) cc_final: 0.7685 (tm-30) REVERT: H 56 LEU cc_start: 0.8657 (mt) cc_final: 0.8067 (pp) REVERT: H 130 GLU cc_start: 0.7804 (tp30) cc_final: 0.7509 (tp30) REVERT: H 137 PHE cc_start: 0.8506 (p90) cc_final: 0.7827 (p90) REVERT: H 149 LEU cc_start: 0.8818 (tp) cc_final: 0.8583 (tp) REVERT: H 163 GLU cc_start: 0.6227 (tp30) cc_final: 0.5755 (tp30) REVERT: H 183 ASN cc_start: 0.8275 (m110) cc_final: 0.8029 (m-40) outliers start: 0 outliers final: 0 residues processed: 923 average time/residue: 0.2079 time to fit residues: 328.1796 Evaluate side-chains 713 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 713 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 237 optimal weight: 2.9990 chunk 364 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 438 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 420 optimal weight: 4.9990 chunk 421 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 198 ASN 2 129 HIS ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 77 GLN ** 6 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 155 GLN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 GLN ** L 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099981 restraints weight = 84178.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100599 restraints weight = 62584.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101034 restraints weight = 53679.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101527 restraints weight = 47363.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101653 restraints weight = 40477.211| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 37137 Z= 0.418 Angle : 2.649 64.643 50632 Z= 1.480 Chirality : 0.445 6.467 5672 Planarity : 0.006 0.093 6377 Dihedral : 6.478 177.334 5099 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.70 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.59 (0.12), residues: 4612 helix: 0.79 (0.10), residues: 2452 sheet: -1.04 (0.30), residues: 291 loop : -1.93 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG 6 94 TYR 0.036 0.002 TYR M 321 PHE 0.044 0.002 PHE 4 150 TRP 0.048 0.002 TRP L 131 HIS 0.011 0.001 HIS 4 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01186 / 0.42 (37100) covalent geometry : angle 2.27168 / 1.48 (50537) SS BOND : bond 0.00583 / 0.31 ( 1) SS BOND : angle 3.35708 / 1.91 ( 2) hydrogen bonds : bond 0.04749 / 3.16 ( 1871) hydrogen bonds : angle 4.90460 / 3.40 ( 5397) metal coordination : bond 0.02261 / 1.44 ( 36) metal coordination : angle 31.88026 / 22.47 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 887 time to evaluate : 1.429 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: 1 91 CYS cc_start: 0.8559 (t) cc_final: 0.8344 (t) REVERT: 1 102 LYS cc_start: 0.8395 (pttt) cc_final: 0.7974 (pttt) REVERT: 1 189 MET cc_start: 0.6389 (mtm) cc_final: 0.6045 (mtm) REVERT: 1 268 MET cc_start: 0.7414 (ttm) cc_final: 0.7161 (ttm) REVERT: 1 270 THR cc_start: 0.8904 (p) cc_final: 0.8378 (t) REVERT: 1 352 SER cc_start: 0.8557 (t) cc_final: 0.8298 (p) REVERT: 1 367 MET cc_start: 0.8615 (tmm) cc_final: 0.8188 (tmm) REVERT: 2 9 ASP cc_start: 0.6823 (m-30) cc_final: 0.6367 (t0) REVERT: 2 28 MET cc_start: 0.8157 (mmm) cc_final: 0.7842 (mmt) REVERT: 2 35 GLN cc_start: 0.8056 (tp40) cc_final: 0.7514 (tm-30) REVERT: 2 36 GLN cc_start: 0.8821 (mt0) cc_final: 0.8067 (mt0) REVERT: 2 141 TYR cc_start: 0.7996 (m-80) cc_final: 0.7217 (m-80) REVERT: 3 47 MET cc_start: 0.8268 (mmm) cc_final: 0.7998 (tpp) REVERT: 3 331 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7033 (tm-30) REVERT: 3 355 LEU cc_start: 0.7090 (tt) cc_final: 0.6561 (tt) REVERT: 3 459 MET cc_start: 0.8176 (mtt) cc_final: 0.7784 (mtm) REVERT: 3 519 GLU cc_start: 0.7481 (tp30) cc_final: 0.6538 (pp20) REVERT: 3 531 LYS cc_start: 0.7014 (mppt) cc_final: 0.6597 (mmtt) REVERT: 3 533 LEU cc_start: 0.8933 (mt) cc_final: 0.8589 (mt) REVERT: 3 655 ARG cc_start: 0.8581 (mpp-170) cc_final: 0.7920 (mtp85) REVERT: 4 74 THR cc_start: 0.9100 (m) cc_final: 0.8831 (p) REVERT: 4 138 LEU cc_start: 0.8771 (tp) cc_final: 0.8302 (tp) REVERT: 4 238 SER cc_start: 0.8938 (m) cc_final: 0.8658 (p) REVERT: 4 271 ASP cc_start: 0.7146 (m-30) cc_final: 0.6698 (m-30) REVERT: 4 274 ASP cc_start: 0.8219 (m-30) cc_final: 0.7782 (m-30) REVERT: 4 364 MET cc_start: 0.8789 (mtm) cc_final: 0.8510 (mtm) REVERT: 5 73 GLU cc_start: 0.7754 (tt0) cc_final: 0.7412 (tm-30) REVERT: 5 117 GLU cc_start: 0.7686 (pp20) cc_final: 0.6984 (pp20) REVERT: 5 122 PHE cc_start: 0.8169 (m-80) cc_final: 0.7725 (m-80) REVERT: 5 170 PHE cc_start: 0.7692 (m-10) cc_final: 0.7298 (m-80) REVERT: 5 177 LYS cc_start: 0.8330 (tttm) cc_final: 0.7913 (tppt) REVERT: 6 25 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8055 (mt-10) REVERT: 6 27 LEU cc_start: 0.8938 (tp) cc_final: 0.8466 (tp) REVERT: 6 86 LYS cc_start: 0.8854 (tptt) cc_final: 0.8573 (tttt) REVERT: 6 92 MET cc_start: 0.8601 (tpp) cc_final: 0.8140 (tpp) REVERT: 6 126 ASN cc_start: 0.8741 (t0) cc_final: 0.8334 (t0) REVERT: 9 3 LEU cc_start: 0.8980 (mt) cc_final: 0.8442 (tp) REVERT: 9 17 LEU cc_start: 0.9196 (tp) cc_final: 0.8897 (tt) REVERT: 9 103 LEU cc_start: 0.9165 (mt) cc_final: 0.8374 (tt) REVERT: 9 105 GLU cc_start: 0.8806 (tt0) cc_final: 0.8325 (tt0) REVERT: 9 121 MET cc_start: 0.8699 (ptp) cc_final: 0.8239 (ptp) REVERT: 9 126 TYR cc_start: 0.7993 (t80) cc_final: 0.7428 (t80) REVERT: 7 21 ARG cc_start: 0.8411 (mtt-85) cc_final: 0.7892 (mtt180) REVERT: 7 86 LEU cc_start: 0.8441 (mp) cc_final: 0.8132 (mp) REVERT: 7 90 HIS cc_start: 0.7352 (p90) cc_final: 0.6501 (t70) REVERT: 7 104 VAL cc_start: 0.8148 (m) cc_final: 0.7900 (p) REVERT: A 56 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7594 (ptt180) REVERT: A 62 TYR cc_start: 0.8021 (t80) cc_final: 0.7764 (t80) REVERT: A 66 MET cc_start: 0.8127 (tmm) cc_final: 0.7626 (tmm) REVERT: J 36 PHE cc_start: 0.7965 (m-10) cc_final: 0.7527 (m-10) REVERT: J 57 ILE cc_start: 0.9140 (tt) cc_final: 0.8907 (tt) REVERT: K 31 ILE cc_start: 0.9228 (tp) cc_final: 0.8969 (tt) REVERT: K 36 ASN cc_start: 0.8387 (m110) cc_final: 0.7798 (m110) REVERT: L 75 PHE cc_start: 0.7285 (t80) cc_final: 0.6931 (t80) REVERT: L 79 ILE cc_start: 0.9016 (mt) cc_final: 0.8668 (mt) REVERT: L 105 PHE cc_start: 0.7616 (m-80) cc_final: 0.7382 (m-80) REVERT: L 114 MET cc_start: 0.8349 (tpt) cc_final: 0.6942 (tpt) REVERT: L 128 PHE cc_start: 0.8027 (t80) cc_final: 0.7656 (t80) REVERT: L 129 ILE cc_start: 0.8098 (mt) cc_final: 0.7833 (mt) REVERT: L 153 ASP cc_start: 0.7821 (m-30) cc_final: 0.7073 (t0) REVERT: L 170 MET cc_start: 0.8599 (mtm) cc_final: 0.8002 (mtm) REVERT: L 225 TRP cc_start: 0.8510 (p-90) cc_final: 0.8114 (p-90) REVERT: L 265 ASP cc_start: 0.7907 (p0) cc_final: 0.6985 (t70) REVERT: L 316 TRP cc_start: 0.7650 (p-90) cc_final: 0.7232 (p-90) REVERT: L 334 LEU cc_start: 0.8417 (mp) cc_final: 0.8065 (mp) REVERT: L 558 ARG cc_start: 0.7669 (mmm160) cc_final: 0.7002 (tmt170) REVERT: L 576 GLN cc_start: 0.8039 (mt0) cc_final: 0.7273 (tm-30) REVERT: M 3 VAL cc_start: 0.8481 (t) cc_final: 0.8131 (p) REVERT: M 16 LEU cc_start: 0.8832 (mt) cc_final: 0.8625 (tp) REVERT: M 103 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7487 (tm-30) REVERT: M 219 GLN cc_start: 0.8839 (mt0) cc_final: 0.8631 (mt0) REVERT: M 221 ASN cc_start: 0.8921 (t0) cc_final: 0.8529 (t0) REVERT: M 282 LYS cc_start: 0.8444 (mtpp) cc_final: 0.7955 (mttm) REVERT: M 293 MET cc_start: 0.8456 (mpp) cc_final: 0.8245 (mpp) REVERT: M 396 PHE cc_start: 0.8156 (m-80) cc_final: 0.7608 (m-80) REVERT: M 432 PHE cc_start: 0.7763 (t80) cc_final: 0.7528 (t80) REVERT: M 443 MET cc_start: 0.8949 (mtp) cc_final: 0.8307 (mtp) REVERT: M 455 HIS cc_start: 0.6589 (t70) cc_final: 0.6326 (t-170) REVERT: N 95 MET cc_start: 0.8832 (mtp) cc_final: 0.8077 (ttm) REVERT: N 103 HIS cc_start: 0.7955 (t-90) cc_final: 0.7340 (t-170) REVERT: N 136 TYR cc_start: 0.8732 (t80) cc_final: 0.8505 (t80) REVERT: N 153 LEU cc_start: 0.9075 (mm) cc_final: 0.8849 (mm) REVERT: N 268 TYR cc_start: 0.7799 (m-80) cc_final: 0.7435 (m-80) REVERT: N 326 PHE cc_start: 0.9302 (t80) cc_final: 0.8543 (t80) REVERT: N 333 LEU cc_start: 0.8867 (mt) cc_final: 0.8562 (tp) REVERT: N 363 LEU cc_start: 0.8685 (mt) cc_final: 0.7715 (tt) REVERT: N 387 GLU cc_start: 0.8411 (tp30) cc_final: 0.7854 (tm-30) REVERT: N 410 LEU cc_start: 0.8970 (pt) cc_final: 0.7887 (tt) REVERT: H 35 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7424 (tm-30) REVERT: H 56 LEU cc_start: 0.8672 (mt) cc_final: 0.8051 (pp) REVERT: H 95 LEU cc_start: 0.8853 (mm) cc_final: 0.8628 (mm) REVERT: H 137 PHE cc_start: 0.8493 (p90) cc_final: 0.7874 (p90) REVERT: H 163 GLU cc_start: 0.6212 (tp30) cc_final: 0.5801 (tp30) REVERT: H 183 ASN cc_start: 0.8299 (m110) cc_final: 0.8020 (m-40) REVERT: H 282 LYS cc_start: 0.8025 (mtmm) cc_final: 0.7763 (mtmm) outliers start: 0 outliers final: 0 residues processed: 887 average time/residue: 0.2094 time to fit residues: 315.7721 Evaluate side-chains 685 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 171 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 386 optimal weight: 1.9990 chunk 372 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 425 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 243 optimal weight: 50.0000 chunk 404 optimal weight: 0.7980 chunk 426 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 147 GLN ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 155 GLN K 36 ASN L 148 ASN ** L 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN H 49 ASN H 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103593 restraints weight = 83211.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104357 restraints weight = 60554.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104851 restraints weight = 49674.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105205 restraints weight = 45566.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105568 restraints weight = 38453.869| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.259 37137 Z= 0.396 Angle : 2.613 62.858 50632 Z= 1.472 Chirality : 0.444 6.414 5672 Planarity : 0.005 0.118 6377 Dihedral : 6.210 178.254 5099 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.27 % Favored : 94.51 % Rotamer: Outliers : 0.03 % Allowed : 1.23 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.30 (0.13), residues: 4612 helix: 0.99 (0.10), residues: 2464 sheet: -0.94 (0.31), residues: 286 loop : -1.73 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG 6 94 TYR 0.041 0.002 TYR M 321 PHE 0.038 0.002 PHE L 382 TRP 0.053 0.001 TRP M 273 HIS 0.027 0.001 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01157 / 0.40 (37100) covalent geometry : angle 2.25207 / 1.47 (50537) SS BOND : bond 0.00455 / 0.24 ( 1) SS BOND : angle 2.86203 / 1.62 ( 2) hydrogen bonds : bond 0.04286 / 2.85 ( 1871) hydrogen bonds : angle 4.70034 / 3.27 ( 5397) metal coordination : bond 0.02022 / 1.25 ( 36) metal coordination : angle 31.00090 / 21.71 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 946 time to evaluate : 1.418 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: 1 91 CYS cc_start: 0.8462 (t) cc_final: 0.8177 (t) REVERT: 1 102 LYS cc_start: 0.7991 (pttt) cc_final: 0.7731 (pttt) REVERT: 1 268 MET cc_start: 0.7320 (ttm) cc_final: 0.7109 (ttm) REVERT: 1 270 THR cc_start: 0.8952 (p) cc_final: 0.8381 (t) REVERT: 1 272 PHE cc_start: 0.7709 (m-80) cc_final: 0.7470 (m-80) REVERT: 1 352 SER cc_start: 0.8565 (t) cc_final: 0.8240 (p) REVERT: 1 367 MET cc_start: 0.8404 (tmm) cc_final: 0.8075 (tmm) REVERT: 2 35 GLN cc_start: 0.7845 (tp40) cc_final: 0.7464 (tm-30) REVERT: 2 36 GLN cc_start: 0.8874 (mt0) cc_final: 0.8056 (mt0) REVERT: 2 141 TYR cc_start: 0.7695 (m-80) cc_final: 0.7005 (m-80) REVERT: 3 47 MET cc_start: 0.8156 (mmm) cc_final: 0.7777 (tpp) REVERT: 3 275 LEU cc_start: 0.9089 (mm) cc_final: 0.8775 (mt) REVERT: 3 331 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7047 (tm-30) REVERT: 3 353 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8263 (mm-30) REVERT: 3 355 LEU cc_start: 0.7303 (tt) cc_final: 0.7067 (tt) REVERT: 3 382 PHE cc_start: 0.7243 (m-10) cc_final: 0.6987 (m-10) REVERT: 3 459 MET cc_start: 0.8048 (mtt) cc_final: 0.7654 (mtm) REVERT: 3 519 GLU cc_start: 0.7390 (tp30) cc_final: 0.6480 (pp20) REVERT: 3 531 LYS cc_start: 0.7093 (mppt) cc_final: 0.6532 (mmtt) REVERT: 3 533 LEU cc_start: 0.9027 (mt) cc_final: 0.8788 (mp) REVERT: 3 655 ARG cc_start: 0.8277 (mpp-170) cc_final: 0.7849 (mtp85) REVERT: 3 710 GLU cc_start: 0.8797 (pm20) cc_final: 0.7637 (pp20) REVERT: 4 67 GLU cc_start: 0.8422 (pm20) cc_final: 0.7910 (pm20) REVERT: 4 121 ASN cc_start: 0.8664 (t0) cc_final: 0.8233 (t0) REVERT: 4 138 LEU cc_start: 0.8691 (tp) cc_final: 0.8236 (tp) REVERT: 4 238 SER cc_start: 0.8934 (m) cc_final: 0.8725 (p) REVERT: 4 271 ASP cc_start: 0.6956 (m-30) cc_final: 0.6561 (m-30) REVERT: 4 274 ASP cc_start: 0.8100 (m-30) cc_final: 0.7707 (m-30) REVERT: 4 282 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6861 (mt-10) REVERT: 4 364 MET cc_start: 0.8819 (mtm) cc_final: 0.8530 (mtm) REVERT: 4 393 MET cc_start: 0.8060 (tmm) cc_final: 0.7776 (tmm) REVERT: 5 48 PHE cc_start: 0.8081 (t80) cc_final: 0.7784 (t80) REVERT: 5 73 GLU cc_start: 0.7641 (tt0) cc_final: 0.7269 (tm-30) REVERT: 5 117 GLU cc_start: 0.7821 (pp20) cc_final: 0.7091 (pp20) REVERT: 5 122 PHE cc_start: 0.8203 (m-80) cc_final: 0.7795 (m-80) REVERT: 5 170 PHE cc_start: 0.7717 (m-10) cc_final: 0.7321 (m-80) REVERT: 5 177 LYS cc_start: 0.8251 (tttm) cc_final: 0.7883 (tppt) REVERT: 6 25 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8059 (mt-10) REVERT: 6 27 LEU cc_start: 0.8908 (tp) cc_final: 0.8555 (tp) REVERT: 6 86 LYS cc_start: 0.8748 (tptt) cc_final: 0.8521 (tttt) REVERT: 6 92 MET cc_start: 0.8498 (tpp) cc_final: 0.7925 (tpp) REVERT: 6 94 ARG cc_start: 0.8010 (tmm-80) cc_final: 0.7441 (ttp-170) REVERT: 6 126 ASN cc_start: 0.8600 (t0) cc_final: 0.8139 (t0) REVERT: 6 134 ASP cc_start: 0.9238 (m-30) cc_final: 0.8912 (m-30) REVERT: 9 3 LEU cc_start: 0.8990 (mt) cc_final: 0.8391 (tp) REVERT: 9 17 LEU cc_start: 0.9163 (tp) cc_final: 0.8839 (tt) REVERT: 9 36 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7991 (mtt-85) REVERT: 9 44 THR cc_start: 0.9045 (p) cc_final: 0.8658 (t) REVERT: 9 103 LEU cc_start: 0.9007 (mt) cc_final: 0.8347 (tt) REVERT: 9 105 GLU cc_start: 0.8834 (tt0) cc_final: 0.8341 (tt0) REVERT: 9 121 MET cc_start: 0.8740 (ptp) cc_final: 0.8276 (ptp) REVERT: 9 126 TYR cc_start: 0.7907 (t80) cc_final: 0.7360 (t80) REVERT: 9 149 GLU cc_start: 0.7769 (tt0) cc_final: 0.7303 (mt-10) REVERT: 7 21 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.7878 (mtt180) REVERT: 7 39 ASP cc_start: 0.9091 (p0) cc_final: 0.8813 (p0) REVERT: 7 86 LEU cc_start: 0.8308 (mp) cc_final: 0.8017 (mp) REVERT: 7 90 HIS cc_start: 0.7098 (p90) cc_final: 0.6528 (t70) REVERT: A 42 MET cc_start: 0.5426 (pmm) cc_final: 0.5045 (pmm) REVERT: A 56 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.7456 (ptt180) REVERT: A 62 TYR cc_start: 0.7981 (t80) cc_final: 0.7745 (t80) REVERT: A 67 LEU cc_start: 0.9188 (tp) cc_final: 0.8604 (mt) REVERT: A 71 PHE cc_start: 0.7994 (m-80) cc_final: 0.7762 (m-80) REVERT: J 39 LEU cc_start: 0.9165 (tp) cc_final: 0.8963 (tp) REVERT: J 54 ILE cc_start: 0.9317 (mm) cc_final: 0.8952 (mm) REVERT: J 57 ILE cc_start: 0.9014 (tt) cc_final: 0.8794 (tt) REVERT: J 59 TYR cc_start: 0.8039 (m-10) cc_final: 0.7459 (m-10) REVERT: J 120 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7863 (mmtt) REVERT: K 36 ASN cc_start: 0.8120 (m-40) cc_final: 0.7696 (m-40) REVERT: K 67 GLU cc_start: 0.8327 (tp30) cc_final: 0.7975 (tp30) REVERT: L 7 ILE cc_start: 0.7733 (mt) cc_final: 0.7482 (mt) REVERT: L 75 PHE cc_start: 0.7159 (t80) cc_final: 0.6700 (t80) REVERT: L 79 ILE cc_start: 0.9092 (mt) cc_final: 0.8713 (mt) REVERT: L 105 PHE cc_start: 0.7717 (m-80) cc_final: 0.7470 (m-80) REVERT: L 114 MET cc_start: 0.8369 (tpt) cc_final: 0.8056 (tpt) REVERT: L 119 VAL cc_start: 0.9303 (m) cc_final: 0.9066 (m) REVERT: L 128 PHE cc_start: 0.8062 (t80) cc_final: 0.7520 (t80) REVERT: L 153 ASP cc_start: 0.7739 (m-30) cc_final: 0.7227 (t0) REVERT: L 167 LEU cc_start: 0.7740 (tp) cc_final: 0.7468 (tp) REVERT: L 225 TRP cc_start: 0.8395 (p-90) cc_final: 0.7941 (p-90) REVERT: L 245 MET cc_start: 0.6584 (mmm) cc_final: 0.6359 (tpt) REVERT: L 265 ASP cc_start: 0.7935 (p0) cc_final: 0.6969 (t70) REVERT: L 415 MET cc_start: 0.8595 (mmt) cc_final: 0.8155 (mmm) REVERT: L 442 MET cc_start: 0.7451 (mtt) cc_final: 0.5781 (mtp) REVERT: L 576 GLN cc_start: 0.7796 (mt0) cc_final: 0.7119 (tm-30) REVERT: M 3 VAL cc_start: 0.8196 (t) cc_final: 0.7859 (p) REVERT: M 39 LEU cc_start: 0.7834 (mm) cc_final: 0.6765 (tp) REVERT: M 102 MET cc_start: 0.7244 (mmp) cc_final: 0.6988 (tpp) REVERT: M 145 LEU cc_start: 0.8540 (tt) cc_final: 0.8316 (tp) REVERT: M 219 GLN cc_start: 0.8845 (mt0) cc_final: 0.8542 (mt0) REVERT: M 221 ASN cc_start: 0.8912 (t0) cc_final: 0.8586 (t0) REVERT: M 282 LYS cc_start: 0.8445 (mtpp) cc_final: 0.7873 (mttm) REVERT: M 377 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7668 (tp30) REVERT: M 396 PHE cc_start: 0.7989 (m-80) cc_final: 0.7469 (m-80) REVERT: M 410 PHE cc_start: 0.8440 (t80) cc_final: 0.7967 (t80) REVERT: M 412 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8110 (ttmt) REVERT: N 3 LEU cc_start: 0.8865 (tp) cc_final: 0.8404 (tp) REVERT: N 9 PHE cc_start: 0.8822 (t80) cc_final: 0.8467 (t80) REVERT: N 13 LEU cc_start: 0.8901 (mm) cc_final: 0.8446 (mm) REVERT: N 15 LEU cc_start: 0.9057 (mt) cc_final: 0.8726 (tt) REVERT: N 95 MET cc_start: 0.8652 (mtp) cc_final: 0.8278 (ttm) REVERT: N 103 HIS cc_start: 0.8032 (t-90) cc_final: 0.7452 (t-170) REVERT: N 124 TRP cc_start: 0.4867 (t-100) cc_final: 0.4642 (t-100) REVERT: N 171 LEU cc_start: 0.9078 (tp) cc_final: 0.8744 (tp) REVERT: N 268 TYR cc_start: 0.7881 (m-80) cc_final: 0.7596 (m-80) REVERT: N 326 PHE cc_start: 0.9230 (t80) cc_final: 0.8451 (t80) REVERT: N 363 LEU cc_start: 0.8672 (mt) cc_final: 0.7735 (tt) REVERT: N 387 GLU cc_start: 0.8497 (tp30) cc_final: 0.8037 (tm-30) REVERT: N 410 LEU cc_start: 0.8900 (pt) cc_final: 0.7941 (tt) REVERT: H 35 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7373 (tm-30) REVERT: H 130 GLU cc_start: 0.7844 (tp30) cc_final: 0.7443 (tp30) REVERT: H 137 PHE cc_start: 0.8355 (p90) cc_final: 0.7627 (p90) REVERT: H 163 GLU cc_start: 0.6293 (tp30) cc_final: 0.5538 (tp30) outliers start: 1 outliers final: 0 residues processed: 947 average time/residue: 0.2073 time to fit residues: 333.7787 Evaluate side-chains 722 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 722 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 365 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 389 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 378 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 306 ASN 6 155 GLN L 148 ASN L 434 HIS N 60 GLN H 49 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099548 restraints weight = 83784.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100412 restraints weight = 62031.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100973 restraints weight = 50714.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101392 restraints weight = 44163.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101591 restraints weight = 39263.824| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.250 37137 Z= 0.428 Angle : 2.664 61.032 50632 Z= 1.485 Chirality : 0.445 6.549 5672 Planarity : 0.006 0.075 6377 Dihedral : 6.394 177.998 5099 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.00 % Favored : 92.74 % Rotamer: Outliers : 0.05 % Allowed : 0.82 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.53 (0.12), residues: 4612 helix: 0.83 (0.10), residues: 2440 sheet: -0.97 (0.32), residues: 263 loop : -1.84 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 6 94 TYR 0.045 0.002 TYR M 321 PHE 0.041 0.002 PHE 4 150 TRP 0.041 0.002 TRP L 420 HIS 0.010 0.002 HIS 4 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01202 / 0.43 (37100) covalent geometry : angle 2.28216 / 1.48 (50537) SS BOND : bond 0.00377 / 0.20 ( 1) SS BOND : angle 2.86079 / 1.61 ( 2) hydrogen bonds : bond 0.04771 / 3.18 ( 1871) hydrogen bonds : angle 4.96433 / 3.44 ( 5397) metal coordination : bond 0.02569 / 1.59 ( 36) metal coordination : angle 32.12711 / 22.79 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 871 time to evaluate : 1.508 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: 1 91 CYS cc_start: 0.8662 (t) cc_final: 0.8411 (t) REVERT: 1 102 LYS cc_start: 0.8282 (pttt) cc_final: 0.7713 (pttt) REVERT: 1 270 THR cc_start: 0.8952 (p) cc_final: 0.8500 (t) REVERT: 1 367 MET cc_start: 0.8633 (tmm) cc_final: 0.8114 (tmm) REVERT: 2 28 MET cc_start: 0.8816 (mmt) cc_final: 0.8391 (mmt) REVERT: 2 35 GLN cc_start: 0.8185 (tp40) cc_final: 0.7663 (tm-30) REVERT: 2 36 GLN cc_start: 0.8818 (mt0) cc_final: 0.8179 (mt0) REVERT: 2 141 TYR cc_start: 0.8054 (m-80) cc_final: 0.7038 (m-80) REVERT: 3 36 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8535 (tm-30) REVERT: 3 47 MET cc_start: 0.8414 (mmm) cc_final: 0.8169 (tpp) REVERT: 3 197 ASP cc_start: 0.8199 (m-30) cc_final: 0.7991 (m-30) REVERT: 3 331 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7107 (tm-30) REVERT: 3 382 PHE cc_start: 0.7424 (m-10) cc_final: 0.7044 (m-10) REVERT: 3 459 MET cc_start: 0.8212 (mtt) cc_final: 0.7820 (mtm) REVERT: 3 519 GLU cc_start: 0.7403 (tp30) cc_final: 0.6492 (pp20) REVERT: 3 531 LYS cc_start: 0.7459 (mppt) cc_final: 0.6659 (mmtt) REVERT: 3 533 LEU cc_start: 0.9019 (mt) cc_final: 0.8748 (mt) REVERT: 3 655 ARG cc_start: 0.8030 (mpp-170) cc_final: 0.7722 (mtp85) REVERT: 4 238 SER cc_start: 0.8971 (m) cc_final: 0.8714 (p) REVERT: 4 271 ASP cc_start: 0.7048 (m-30) cc_final: 0.6649 (m-30) REVERT: 4 274 ASP cc_start: 0.8169 (m-30) cc_final: 0.7877 (m-30) REVERT: 4 364 MET cc_start: 0.8856 (mtm) cc_final: 0.8615 (mtm) REVERT: 4 393 MET cc_start: 0.7945 (tmm) cc_final: 0.7648 (ttp) REVERT: 5 73 GLU cc_start: 0.7804 (tt0) cc_final: 0.7305 (tm-30) REVERT: 5 117 GLU cc_start: 0.7932 (pp20) cc_final: 0.7011 (pp20) REVERT: 5 122 PHE cc_start: 0.8114 (m-80) cc_final: 0.7668 (m-80) REVERT: 5 177 LYS cc_start: 0.8355 (tttm) cc_final: 0.7946 (tppt) REVERT: 6 25 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7914 (mt-10) REVERT: 6 27 LEU cc_start: 0.8899 (tp) cc_final: 0.8449 (tp) REVERT: 6 86 LYS cc_start: 0.8859 (tptt) cc_final: 0.8591 (tttt) REVERT: 6 92 MET cc_start: 0.8619 (tpp) cc_final: 0.8108 (tpp) REVERT: 6 94 ARG cc_start: 0.8142 (tmm-80) cc_final: 0.7448 (ttp-170) REVERT: 6 126 ASN cc_start: 0.8806 (t0) cc_final: 0.8371 (t0) REVERT: 6 133 VAL cc_start: 0.8643 (t) cc_final: 0.8430 (t) REVERT: 9 3 LEU cc_start: 0.8988 (mt) cc_final: 0.8457 (tp) REVERT: 9 17 LEU cc_start: 0.9082 (tp) cc_final: 0.8793 (tt) REVERT: 9 36 ARG cc_start: 0.8290 (mtt180) cc_final: 0.8000 (mtt-85) REVERT: 9 103 LEU cc_start: 0.9280 (mt) cc_final: 0.8752 (tp) REVERT: 9 105 GLU cc_start: 0.8853 (tt0) cc_final: 0.8421 (tt0) REVERT: 9 121 MET cc_start: 0.8747 (ptp) cc_final: 0.8248 (ptp) REVERT: 9 126 TYR cc_start: 0.8040 (t80) cc_final: 0.7590 (t80) REVERT: 7 21 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.8026 (mtt180) REVERT: 7 39 ASP cc_start: 0.9256 (p0) cc_final: 0.8989 (p0) REVERT: 7 86 LEU cc_start: 0.8423 (mp) cc_final: 0.8078 (mt) REVERT: 7 90 HIS cc_start: 0.7327 (p90) cc_final: 0.6469 (t70) REVERT: A 42 MET cc_start: 0.5602 (pmm) cc_final: 0.5231 (pmm) REVERT: A 56 ARG cc_start: 0.8085 (tpp-160) cc_final: 0.7595 (ptt180) REVERT: A 66 MET cc_start: 0.7436 (tmm) cc_final: 0.7013 (tmm) REVERT: A 67 LEU cc_start: 0.9281 (tp) cc_final: 0.9041 (mt) REVERT: A 72 ASP cc_start: 0.8341 (t70) cc_final: 0.8035 (t70) REVERT: J 39 LEU cc_start: 0.9142 (tp) cc_final: 0.8818 (tp) REVERT: J 54 ILE cc_start: 0.9304 (mm) cc_final: 0.8993 (mm) REVERT: J 57 ILE cc_start: 0.9135 (tt) cc_final: 0.8890 (tt) REVERT: J 59 TYR cc_start: 0.8049 (m-10) cc_final: 0.7386 (m-10) REVERT: J 120 LYS cc_start: 0.8329 (mtmm) cc_final: 0.7928 (mmtt) REVERT: J 139 LEU cc_start: 0.9257 (tp) cc_final: 0.9036 (tt) REVERT: K 36 ASN cc_start: 0.7979 (m-40) cc_final: 0.7205 (m-40) REVERT: L 7 ILE cc_start: 0.7814 (mt) cc_final: 0.7571 (mt) REVERT: L 75 PHE cc_start: 0.7219 (t80) cc_final: 0.6909 (t80) REVERT: L 79 ILE cc_start: 0.9132 (mt) cc_final: 0.8769 (mt) REVERT: L 114 MET cc_start: 0.8455 (tpt) cc_final: 0.8060 (tpt) REVERT: L 170 MET cc_start: 0.8662 (mtm) cc_final: 0.8380 (mtm) REVERT: L 214 VAL cc_start: 0.8856 (t) cc_final: 0.8612 (t) REVERT: L 225 TRP cc_start: 0.8453 (p-90) cc_final: 0.7996 (p-90) REVERT: L 265 ASP cc_start: 0.7875 (p0) cc_final: 0.7028 (t70) REVERT: L 316 TRP cc_start: 0.7824 (p-90) cc_final: 0.7393 (p-90) REVERT: L 415 MET cc_start: 0.8517 (mmt) cc_final: 0.8094 (mmm) REVERT: L 442 MET cc_start: 0.7420 (mtt) cc_final: 0.5865 (mtp) REVERT: L 576 GLN cc_start: 0.8064 (mt0) cc_final: 0.7241 (tm-30) REVERT: M 3 VAL cc_start: 0.8326 (t) cc_final: 0.8011 (p) REVERT: M 102 MET cc_start: 0.7606 (mmp) cc_final: 0.7279 (tpp) REVERT: M 145 LEU cc_start: 0.8647 (tt) cc_final: 0.8417 (tp) REVERT: M 208 PHE cc_start: 0.8077 (t80) cc_final: 0.7786 (t80) REVERT: M 219 GLN cc_start: 0.8815 (mt0) cc_final: 0.8608 (mt0) REVERT: M 221 ASN cc_start: 0.8989 (t0) cc_final: 0.8600 (t0) REVERT: M 282 LYS cc_start: 0.8487 (mtpp) cc_final: 0.7947 (mttm) REVERT: M 314 LEU cc_start: 0.9363 (tp) cc_final: 0.9137 (tp) REVERT: M 377 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7736 (tp30) REVERT: M 396 PHE cc_start: 0.8169 (m-80) cc_final: 0.7567 (m-80) REVERT: M 410 PHE cc_start: 0.8528 (t80) cc_final: 0.8089 (t80) REVERT: M 412 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8096 (ttmt) REVERT: M 443 MET cc_start: 0.9029 (mtp) cc_final: 0.8723 (mtp) REVERT: N 15 LEU cc_start: 0.9074 (mt) cc_final: 0.8736 (tt) REVERT: N 95 MET cc_start: 0.8903 (mtp) cc_final: 0.8072 (ttm) REVERT: N 103 HIS cc_start: 0.8201 (t-90) cc_final: 0.7497 (t-170) REVERT: N 171 LEU cc_start: 0.9276 (tp) cc_final: 0.9027 (tp) REVERT: N 268 TYR cc_start: 0.7880 (m-80) cc_final: 0.7610 (m-80) REVERT: N 330 MET cc_start: 0.8947 (mmp) cc_final: 0.8698 (mmp) REVERT: N 363 LEU cc_start: 0.7908 (mt) cc_final: 0.7707 (tt) REVERT: N 368 SER cc_start: 0.8609 (p) cc_final: 0.8346 (p) REVERT: N 387 GLU cc_start: 0.8413 (tp30) cc_final: 0.7985 (tm-30) REVERT: N 410 LEU cc_start: 0.8981 (pt) cc_final: 0.7968 (tt) REVERT: H 35 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7341 (tm-30) REVERT: H 39 LEU cc_start: 0.9308 (mm) cc_final: 0.9108 (mm) REVERT: H 56 LEU cc_start: 0.8682 (mt) cc_final: 0.8065 (pp) REVERT: H 137 PHE cc_start: 0.8635 (p90) cc_final: 0.7989 (p90) REVERT: H 163 GLU cc_start: 0.6263 (tp30) cc_final: 0.5830 (tp30) REVERT: H 281 LEU cc_start: 0.8465 (mt) cc_final: 0.8239 (mt) REVERT: H 282 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7564 (mtmm) outliers start: 2 outliers final: 0 residues processed: 873 average time/residue: 0.2103 time to fit residues: 313.8775 Evaluate side-chains 687 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 424 optimal weight: 5.9990 chunk 452 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 chunk 394 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 342 optimal weight: 8.9990 chunk 256 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 74 GLN 3 428 HIS ** 6 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 155 GLN 7 94 HIS L 148 ASN L 434 HIS M 455 HIS N 60 GLN N 279 GLN H 49 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104111 restraints weight = 83559.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104982 restraints weight = 58668.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105322 restraints weight = 50596.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105697 restraints weight = 46261.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105969 restraints weight = 38514.279| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.259 37137 Z= 0.397 Angle : 2.618 75.089 50632 Z= 1.472 Chirality : 0.444 6.479 5672 Planarity : 0.005 0.067 6377 Dihedral : 6.149 178.729 5099 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.31 % Favored : 94.49 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.33 (0.13), residues: 4612 helix: 0.98 (0.10), residues: 2442 sheet: -1.06 (0.30), residues: 291 loop : -1.72 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 6 94 TYR 0.045 0.002 TYR M 321 PHE 0.030 0.002 PHE M 241 TRP 0.042 0.001 TRP L 420 HIS 0.009 0.001 HIS 1 87 Details of bonding type rmsd/Z covalent geometry : bond 0.01159 / 0.40 (37100) covalent geometry : angle 2.25607 / 1.47 (50537) SS BOND : bond 0.00389 / 0.20 ( 1) SS BOND : angle 2.88183 / 1.62 ( 2) hydrogen bonds : bond 0.04212 / 2.82 ( 1871) hydrogen bonds : angle 4.71444 / 3.28 ( 5397) metal coordination : bond 0.02134 / 1.40 ( 36) metal coordination : angle 31.07400 / 21.59 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 902 time to evaluate : 1.632 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: 1 91 CYS cc_start: 0.8580 (t) cc_final: 0.8213 (t) REVERT: 1 102 LYS cc_start: 0.7921 (pttt) cc_final: 0.7419 (pttt) REVERT: 1 103 ASP cc_start: 0.9174 (m-30) cc_final: 0.8737 (m-30) REVERT: 1 270 THR cc_start: 0.8713 (p) cc_final: 0.8139 (t) REVERT: 1 311 MET cc_start: 0.8333 (mtm) cc_final: 0.7821 (mtm) REVERT: 1 367 MET cc_start: 0.8469 (tmm) cc_final: 0.7984 (tmm) REVERT: 2 28 MET cc_start: 0.8580 (mmt) cc_final: 0.8286 (mmt) REVERT: 2 35 GLN cc_start: 0.8042 (tp40) cc_final: 0.7630 (tm-30) REVERT: 2 36 GLN cc_start: 0.8927 (mt0) cc_final: 0.8228 (mt0) REVERT: 2 141 TYR cc_start: 0.6948 (m-80) cc_final: 0.6709 (m-10) REVERT: 3 47 MET cc_start: 0.8085 (mmm) cc_final: 0.7740 (tpp) REVERT: 3 113 LEU cc_start: 0.9320 (tp) cc_final: 0.9086 (tp) REVERT: 3 275 LEU cc_start: 0.9043 (mm) cc_final: 0.8740 (mt) REVERT: 3 310 LEU cc_start: 0.7686 (mm) cc_final: 0.7284 (mt) REVERT: 3 331 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7097 (tm-30) REVERT: 3 353 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8299 (mm-30) REVERT: 3 459 MET cc_start: 0.8079 (mtt) cc_final: 0.7719 (mtm) REVERT: 3 519 GLU cc_start: 0.7220 (tp30) cc_final: 0.6419 (pp20) REVERT: 3 531 LYS cc_start: 0.7122 (mppt) cc_final: 0.6582 (mmtt) REVERT: 3 533 LEU cc_start: 0.8949 (mt) cc_final: 0.8633 (mp) REVERT: 3 558 TRP cc_start: 0.7684 (p90) cc_final: 0.7425 (p90) REVERT: 3 655 ARG cc_start: 0.7961 (mpp-170) cc_final: 0.7759 (mtp85) REVERT: 3 710 GLU cc_start: 0.8792 (pm20) cc_final: 0.7678 (pp20) REVERT: 4 67 GLU cc_start: 0.8423 (pm20) cc_final: 0.7882 (pm20) REVERT: 4 121 ASN cc_start: 0.8619 (t0) cc_final: 0.8141 (t0) REVERT: 4 130 LEU cc_start: 0.9401 (mm) cc_final: 0.8992 (mt) REVERT: 4 271 ASP cc_start: 0.6885 (m-30) cc_final: 0.6458 (m-30) REVERT: 4 274 ASP cc_start: 0.8175 (m-30) cc_final: 0.7835 (m-30) REVERT: 4 282 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7024 (mt-10) REVERT: 4 364 MET cc_start: 0.8898 (mtm) cc_final: 0.8627 (mtm) REVERT: 4 393 MET cc_start: 0.7912 (tmm) cc_final: 0.7583 (ttp) REVERT: 5 48 PHE cc_start: 0.8058 (t80) cc_final: 0.7759 (t80) REVERT: 5 73 GLU cc_start: 0.7685 (tt0) cc_final: 0.7282 (tm-30) REVERT: 5 117 GLU cc_start: 0.7909 (pp20) cc_final: 0.7071 (pp20) REVERT: 5 122 PHE cc_start: 0.8154 (m-80) cc_final: 0.7699 (m-80) REVERT: 5 177 LYS cc_start: 0.8308 (tttm) cc_final: 0.7896 (tppt) REVERT: 6 25 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8096 (mt-10) REVERT: 6 27 LEU cc_start: 0.8933 (tp) cc_final: 0.8544 (tp) REVERT: 6 86 LYS cc_start: 0.8778 (tptt) cc_final: 0.8540 (tttt) REVERT: 6 92 MET cc_start: 0.8472 (tpp) cc_final: 0.7969 (tpp) REVERT: 6 94 ARG cc_start: 0.8173 (tmm-80) cc_final: 0.7947 (ttp-170) REVERT: 6 126 ASN cc_start: 0.8198 (t0) cc_final: 0.7684 (t0) REVERT: 6 134 ASP cc_start: 0.9246 (m-30) cc_final: 0.8982 (m-30) REVERT: 9 3 LEU cc_start: 0.8951 (mt) cc_final: 0.8395 (tp) REVERT: 9 17 LEU cc_start: 0.9152 (tp) cc_final: 0.8770 (tt) REVERT: 9 36 ARG cc_start: 0.8238 (mtt180) cc_final: 0.8010 (mtt-85) REVERT: 9 44 THR cc_start: 0.9014 (p) cc_final: 0.8698 (t) REVERT: 9 79 ASN cc_start: 0.8236 (m-40) cc_final: 0.7830 (m-40) REVERT: 9 103 LEU cc_start: 0.8994 (mt) cc_final: 0.8282 (tt) REVERT: 9 105 GLU cc_start: 0.8764 (tt0) cc_final: 0.8166 (tt0) REVERT: 9 121 MET cc_start: 0.8676 (ptp) cc_final: 0.7969 (ptp) REVERT: 9 126 TYR cc_start: 0.7965 (t80) cc_final: 0.7549 (t80) REVERT: 9 153 THR cc_start: 0.8474 (m) cc_final: 0.8251 (t) REVERT: 7 17 LEU cc_start: 0.8735 (pp) cc_final: 0.8501 (tp) REVERT: 7 21 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.7916 (mtt180) REVERT: 7 86 LEU cc_start: 0.8288 (mp) cc_final: 0.7981 (mp) REVERT: 7 90 HIS cc_start: 0.7122 (p90) cc_final: 0.6836 (t70) REVERT: A 56 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7429 (ptt180) REVERT: A 67 LEU cc_start: 0.9258 (tp) cc_final: 0.8936 (mt) REVERT: A 103 LEU cc_start: 0.8922 (mm) cc_final: 0.7959 (mm) REVERT: A 116 MET cc_start: 0.6745 (ppp) cc_final: 0.6347 (ppp) REVERT: J 36 PHE cc_start: 0.8068 (m-10) cc_final: 0.7825 (m-10) REVERT: J 54 ILE cc_start: 0.9379 (mm) cc_final: 0.9046 (mm) REVERT: J 57 ILE cc_start: 0.8952 (tt) cc_final: 0.8732 (tt) REVERT: J 120 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7833 (mmtt) REVERT: K 36 ASN cc_start: 0.8037 (m-40) cc_final: 0.7669 (m-40) REVERT: L 75 PHE cc_start: 0.7171 (t80) cc_final: 0.6847 (t80) REVERT: L 79 ILE cc_start: 0.9316 (mt) cc_final: 0.8958 (mt) REVERT: L 114 MET cc_start: 0.8482 (tpt) cc_final: 0.7862 (tpt) REVERT: L 128 PHE cc_start: 0.8227 (t80) cc_final: 0.7763 (t80) REVERT: L 132 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7361 (mm-30) REVERT: L 153 ASP cc_start: 0.7627 (m-30) cc_final: 0.7181 (t0) REVERT: L 225 TRP cc_start: 0.8379 (p-90) cc_final: 0.7876 (p-90) REVERT: L 245 MET cc_start: 0.6588 (mmm) cc_final: 0.6153 (tpt) REVERT: L 265 ASP cc_start: 0.7924 (p0) cc_final: 0.7235 (t70) REVERT: L 286 PHE cc_start: 0.5289 (p90) cc_final: 0.4737 (p90) REVERT: L 415 MET cc_start: 0.8522 (mmt) cc_final: 0.8151 (mmm) REVERT: L 442 MET cc_start: 0.7299 (mtt) cc_final: 0.5709 (mtp) REVERT: L 576 GLN cc_start: 0.7769 (mt0) cc_final: 0.7120 (tm-30) REVERT: M 39 LEU cc_start: 0.7841 (mm) cc_final: 0.6795 (tp) REVERT: M 102 MET cc_start: 0.7719 (mmp) cc_final: 0.7264 (tpp) REVERT: M 103 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6567 (tm-30) REVERT: M 219 GLN cc_start: 0.8812 (mt0) cc_final: 0.8386 (mt0) REVERT: M 322 THR cc_start: 0.8295 (m) cc_final: 0.8011 (t) REVERT: M 377 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7792 (tp30) REVERT: M 396 PHE cc_start: 0.7948 (m-80) cc_final: 0.7345 (m-80) REVERT: M 410 PHE cc_start: 0.8390 (t80) cc_final: 0.7986 (t80) REVERT: M 412 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8159 (ttmt) REVERT: N 13 LEU cc_start: 0.8891 (mm) cc_final: 0.8496 (mm) REVERT: N 15 LEU cc_start: 0.9057 (mt) cc_final: 0.8791 (tt) REVERT: N 95 MET cc_start: 0.8770 (mtp) cc_final: 0.8207 (ttm) REVERT: N 103 HIS cc_start: 0.8082 (t-90) cc_final: 0.7403 (t-170) REVERT: N 171 LEU cc_start: 0.9018 (tp) cc_final: 0.8692 (tp) REVERT: N 268 TYR cc_start: 0.7705 (m-80) cc_final: 0.7456 (m-80) REVERT: N 326 PHE cc_start: 0.9253 (t80) cc_final: 0.8424 (t80) REVERT: N 330 MET cc_start: 0.8883 (mmp) cc_final: 0.8618 (mmp) REVERT: N 363 LEU cc_start: 0.8643 (mt) cc_final: 0.7758 (tt) REVERT: N 387 GLU cc_start: 0.8531 (tp30) cc_final: 0.8254 (tm-30) REVERT: N 410 LEU cc_start: 0.8902 (pt) cc_final: 0.8007 (tt) REVERT: H 18 LEU cc_start: 0.9129 (tp) cc_final: 0.8928 (tp) REVERT: H 24 LEU cc_start: 0.8409 (mt) cc_final: 0.7548 (pp) REVERT: H 49 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.8774 (p0) REVERT: H 56 LEU cc_start: 0.8626 (mt) cc_final: 0.8083 (pp) REVERT: H 130 GLU cc_start: 0.7739 (tp30) cc_final: 0.7346 (tp30) REVERT: H 137 PHE cc_start: 0.8496 (p90) cc_final: 0.7788 (p90) REVERT: H 182 LEU cc_start: 0.9186 (mm) cc_final: 0.8825 (mt) REVERT: H 187 ASN cc_start: 0.8388 (m-40) cc_final: 0.7994 (m110) outliers start: 1 outliers final: 0 residues processed: 903 average time/residue: 0.2103 time to fit residues: 324.4165 Evaluate side-chains 712 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 711 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 328 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 370 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 392 optimal weight: 0.1980 chunk 282 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 384 optimal weight: 0.0170 chunk 172 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 386 ASN ** 6 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 155 GLN L 148 ASN M 292 HIS N 60 GLN H 117 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104157 restraints weight = 83010.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105023 restraints weight = 59143.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106245 restraints weight = 49526.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106759 restraints weight = 39459.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106982 restraints weight = 31800.928| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.257 37137 Z= 0.396 Angle : 2.615 75.781 50632 Z= 1.471 Chirality : 0.444 6.445 5672 Planarity : 0.005 0.077 6377 Dihedral : 6.005 176.912 5099 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.66 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.23 (0.13), residues: 4612 helix: 1.07 (0.11), residues: 2444 sheet: -1.09 (0.29), residues: 304 loop : -1.66 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 6 94 TYR 0.029 0.002 TYR H 147 PHE 0.041 0.002 PHE L 328 TRP 0.042 0.001 TRP L 420 HIS 0.015 0.001 HIS H 192 Details of bonding type rmsd/Z covalent geometry : bond 0.01159 / 0.40 (37100) covalent geometry : angle 2.25243 / 1.47 (50537) SS BOND : bond 0.00340 / 0.18 ( 1) SS BOND : angle 2.69879 / 1.51 ( 2) hydrogen bonds : bond 0.04137 / 2.76 ( 1871) hydrogen bonds : angle 4.65383 / 3.24 ( 5397) metal coordination : bond 0.01962 / 1.28 ( 36) metal coordination : angle 31.09583 / 21.52 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7398.79 seconds wall clock time: 128 minutes 7.57 seconds (7687.57 seconds total)