Starting phenix.real_space_refine on Tue Sep 15 04:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zjl_11235/09_2026/6zjl_11235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zjl_11235/09_2026/6zjl_11235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zjl_11235/09_2026/6zjl_11235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zjl_11235/09_2026/6zjl_11235.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6zjl_11235/09_2026/6zjl_11235.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zjl_11235/09_2026/6zjl_11235.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zjl_11235/09_2026/6zjl_11235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zjl_11235/09_2026/6zjl_11235.cif" } resolution = 4.3 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= 0.039 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 1 5.49 5 S 180 5.16 5 C 23625 2.51 5 N 5998 2.21 5 O 6221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 338 residue(s): 0.03s 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: 36057 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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 1 356 113.472 70.680 223.270 1.00 50.00 S ATOM 2792 SG CYS 1 359 117.693 72.814 225.970 1.00 50.00 S ATOM 3102 SG CYS 1 400 112.357 70.375 228.915 1.00 50.00 S ATOM 2753 SG CYS 1 353 116.038 66.609 226.824 1.00 50.00 S ATOM 4091 SG CYS 2 83 128.181 73.951 243.535 1.00 50.00 S ATOM 4123 SG CYS 2 88 129.412 76.425 245.982 1.00 50.00 S ATOM 4394 SG CYS 2 124 123.487 74.850 243.815 1.00 50.00 S ATOM 4418 SG CYS 2 128 123.505 77.246 246.365 1.00 50.00 S ATOM 5640 SG CYS 3 128 121.009 66.516 203.662 1.00 50.00 S ATOM 5584 SG CYS 3 119 125.918 69.768 201.811 1.00 50.00 S ATOM 5604 SG CYS 3 122 126.520 63.777 203.146 1.00 50.00 S ATOM 6083 SG CYS 3 184 115.923 61.659 213.032 1.00 50.00 S ATOM 6059 SG CYS 3 181 122.185 62.242 214.338 1.00 50.00 S ATOM 6109 SG CYS 3 187 118.661 56.979 214.324 1.00 50.00 S ATOM 6445 SG CYS 3 230 120.037 60.271 209.043 1.00 50.00 S ATOM 6652 SG CYS 3 256 112.923 41.114 197.082 1.00 50.00 S ATOM 6918 SG CYS 3 291 114.235 40.927 203.195 1.00 50.00 S ATOM 6695 SG CYS 3 263 108.931 43.436 200.557 1.00 50.00 S ATOM 6671 SG CYS 3 259 109.787 37.373 200.872 1.00 50.00 S ATOM 5085 SG CYS 3 34 110.237 65.190 215.142 1.00 50.00 S ATOM 5163 SG CYS 3 45 112.042 68.209 213.331 1.00 50.00 S ATOM 5188 SG CYS 3 48 106.522 69.811 213.756 1.00 50.00 S ATOM 5320 SG CYS 3 83 106.083 67.183 214.984 1.00 50.00 S ATOM 16119 SG CYS 6 111 125.549 73.176 167.027 1.00 50.00 S ATOM 15614 SG CYS 6 46 130.127 75.855 164.202 1.00 50.00 S ATOM 15608 SG CYS 6 45 125.811 79.188 165.859 1.00 50.00 S ATOM 16328 SG CYS 6 140 128.893 76.622 170.582 1.00 50.00 S ATOM 17432 SG CYS 9 101 128.717 75.342 178.757 1.00 50.00 S ATOM 17407 SG CYS 9 98 132.927 71.881 176.396 1.00 50.00 S ATOM 17450 SG CYS 9 104 132.766 73.575 182.746 1.00 50.00 S ATOM 17129 SG CYS 9 63 128.380 69.874 180.032 1.00 50.00 S ATOM 17479 SG CYS 9 108 135.660 72.152 191.041 1.00 50.00 S ATOM 17108 SG CYS 9 59 132.870 68.620 187.221 1.00 50.00 S ATOM 17070 SG CYS 9 53 138.071 66.482 190.851 1.00 50.00 S ATOM 17088 SG CYS 9 56 132.113 68.376 192.922 1.00 50.00 S Time building chain proxies: 7.02, per 1000 atoms: 0.19 Number of scatterers: 36057 At special positions: 0 Unit cell: (177.16, 134.16, 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 1 15.00 O 6221 8.00 N 5998 7.00 C 23625 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=2.05 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 201 " pdb="FE2 FES 2 201 " - pdb=" SG CYS 2 128 " pdb="FE2 FES 2 201 " - pdb=" SG CYS 2 124 " pdb="FE1 FES 2 201 " - pdb=" SG CYS 2 83 " pdb="FE1 FES 2 201 " - pdb=" SG CYS 2 88 " pdb=" FES 3 804 " pdb="FE2 FES 3 804 " - pdb=" SG CYS 3 48 " pdb="FE2 FES 3 804 " - pdb=" SG CYS 3 83 " pdb="FE1 FES 3 804 " - pdb=" SG CYS 3 34 " pdb="FE1 FES 3 804 " - pdb=" SG CYS 3 45 " 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="FE2 SF4 3 802 " - pdb=" SG CYS 3 181 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 230 " 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="FE2 SF4 6 201 " - pdb=" SG CYS 6 46 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 45 " 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="FE2 SF4 9 201 " - pdb=" SG CYS 9 98 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 101 " pdb="FE3 SF4 9 201 " - pdb=" NE2 HIS 9 41 " pdb=" SF4 9 202 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 53 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 56 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 59 " 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: 196 helices and 26 sheets defined 58.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain '1' and resid 28 through 34 Processing helix chain '1' and resid 38 through 48 Processing helix chain '1' and resid 49 through 61 removed outlier: 3.831A pdb=" N VAL 1 57 " --> pdb=" O VAL 1 53 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG 1 59 " --> pdb=" O GLU 1 55 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY 1 61 " --> pdb=" O VAL 1 57 " (cutoff:3.500A) Processing helix chain '1' and resid 71 through 78 removed outlier: 3.715A pdb=" N LYS 1 75 " --> pdb=" O PRO 1 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE 1 78 " --> pdb=" O LEU 1 74 " (cutoff:3.500A) Processing helix chain '1' and resid 101 through 110 removed outlier: 4.592A pdb=" N TYR 1 105 " --> pdb=" O PHE 1 101 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE 1 106 " --> pdb=" O LYS 1 102 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL 1 110 " --> pdb=" O ILE 1 106 " (cutoff:3.500A) Processing helix chain '1' and resid 110 through 125 removed outlier: 3.983A 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: 3.888A pdb=" N MET 1 189 " --> pdb=" O GLU 1 185 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.719A pdb=" N ILE 1 230 " --> pdb=" O SER 1 226 " (cutoff:3.500A) Processing helix chain '1' and resid 234 through 240 removed outlier: 3.761A pdb=" N PHE 1 238 " --> pdb=" O GLY 1 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN 1 240 " --> pdb=" O ASP 1 236 " (cutoff:3.500A) Processing helix chain '1' and resid 271 through 278 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 351 removed outlier: 3.573A pdb=" N ASN 1 343 " --> pdb=" O ASP 1 339 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS 1 350 " --> pdb=" O ARG 1 346 " (cutoff:3.500A) Processing helix chain '1' and resid 356 through 366 removed outlier: 3.778A pdb=" N VAL 1 363 " --> pdb=" O CYS 1 359 " (cutoff:3.500A) Processing helix chain '1' and resid 366 through 375 Processing helix chain '1' and resid 380 through 396 removed outlier: 3.927A pdb=" N VAL 1 384 " --> pdb=" O GLU 1 380 " (cutoff:3.500A) Proline residue: 1 392 - end of helix removed outlier: 4.290A pdb=" N GLY 1 396 " --> pdb=" O PRO 1 392 " (cutoff:3.500A) Processing helix chain '1' and resid 401 through 417 Proline residue: 1 409 - end of helix removed outlier: 3.521A pdb=" N LEU 1 414 " --> pdb=" O VAL 1 410 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG 1 415 " --> pdb=" O LYS 1 411 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS 1 416 " --> pdb=" O GLY 1 412 " (cutoff:3.500A) Processing helix chain '1' and resid 417 through 427 removed outlier: 3.958A pdb=" N TYR 1 421 " --> pdb=" O PHE 1 417 " (cutoff:3.500A) Processing helix chain '2' and resid 7 through 17 removed outlier: 4.195A pdb=" N LYS 2 17 " --> pdb=" O GLU 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 22 through 25 removed outlier: 3.523A pdb=" N ALA 2 25 " --> pdb=" O GLY 2 22 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 22 through 25' Processing helix chain '2' and resid 26 through 39 Processing helix chain '2' and resid 42 through 54 Processing helix chain '2' and resid 56 through 65 removed outlier: 3.713A 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 Processing helix chain '2' and resid 127 through 131 removed outlier: 3.630A pdb=" N THR 2 130 " --> pdb=" O SER 2 127 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 159 Processing helix chain '3' and resid 18 through 26 removed outlier: 3.572A pdb=" N ALA 3 22 " --> pdb=" O SER 3 18 " (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 185 through 194 Processing helix chain '3' and resid 205 through 209 removed outlier: 3.788A 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: 3.730A 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 321 through 332 Processing helix chain '3' and resid 350 through 364 Processing helix chain '3' and resid 401 through 406 Processing helix chain '3' and resid 408 through 418 Processing helix chain '3' and resid 457 through 462 removed outlier: 3.859A pdb=" N LYS 3 460 " --> pdb=" O PRO 3 457 " (cutoff:3.500A) Processing helix chain '3' and resid 472 through 482 removed outlier: 4.122A 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: 4.288A pdb=" N LEU 3 512 " --> pdb=" O GLY 3 508 " (cutoff:3.500A) Processing helix chain '3' and resid 514 through 528 removed outlier: 3.653A pdb=" N ALA 3 518 " --> pdb=" O ASP 3 514 " (cutoff:3.500A) removed outlier: 4.154A 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 removed outlier: 3.972A pdb=" N LEU 3 577 " --> pdb=" O PRO 3 573 " (cutoff:3.500A) Processing helix chain '3' and resid 606 through 610 Processing helix chain '3' and resid 636 through 648 removed outlier: 3.571A pdb=" N VAL 3 640 " --> pdb=" O GLY 3 636 " (cutoff:3.500A) Processing helix chain '3' and resid 656 through 668 removed outlier: 3.687A pdb=" N ALA 3 660 " --> pdb=" O LEU 3 656 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN 3 661 " --> pdb=" O HIS 3 657 " (cutoff:3.500A) Processing helix chain '3' and resid 700 through 704 removed outlier: 3.612A pdb=" N ALA 3 704 " --> pdb=" O ALA 3 701 " (cutoff:3.500A) Processing helix chain '3' and resid 707 through 712 removed outlier: 4.744A 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: 3.551A 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 74 through 79 removed outlier: 3.721A pdb=" N ILE 4 79 " --> pdb=" O TYR 4 75 " (cutoff:3.500A) Processing helix chain '4' and resid 80 through 85 Proline residue: 4 83 - end of helix No H-bonds generated for 'chain '4' and resid 80 through 85' Processing helix chain '4' and resid 90 through 106 removed outlier: 3.654A pdb=" N ASP 4 94 " --> pdb=" O SER 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 110 through 140 removed outlier: 3.580A pdb=" N GLU 4 114 " --> pdb=" O PRO 4 110 " (cutoff:3.500A) Processing helix chain '4' and resid 144 through 165 removed outlier: 4.152A pdb=" N TYR 4 148 " --> pdb=" O THR 4 144 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG 4 153 " --> pdb=" O ALA 4 149 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL 4 163 " --> pdb=" O LEU 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 209 removed outlier: 3.502A pdb=" N VAL 4 196 " --> pdb=" O LYS 4 192 " (cutoff:3.500A) Proline residue: 4 198 - end of helix removed outlier: 3.695A pdb=" N GLU 4 203 " --> pdb=" O HIS 4 199 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR 4 204 " --> pdb=" O ARG 4 200 " (cutoff:3.500A) Processing helix chain '4' and resid 211 through 219 removed outlier: 3.822A 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 239 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: 3.520A pdb=" N ARG 4 279 " --> pdb=" O ARG 4 275 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE 4 280 " --> pdb=" O MET 4 276 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG 4 284 " --> pdb=" O ILE 4 280 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU 4 295 " --> pdb=" O LYS 4 291 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG 4 296 " --> pdb=" O GLN 4 292 " (cutoff:3.500A) Processing helix chain '4' and resid 320 through 333 removed outlier: 3.639A pdb=" N VAL 4 324 " --> pdb=" O SER 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 372 through 378 removed outlier: 4.004A pdb=" N VAL 4 376 " --> pdb=" O ALA 4 372 " (cutoff:3.500A) Processing helix chain '4' and resid 380 through 385 Processing helix chain '4' and resid 392 through 401 removed outlier: 3.780A pdb=" N ILE 4 397 " --> pdb=" O MET 4 393 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 4 400 " --> pdb=" O ILE 4 396 " (cutoff:3.500A) Processing helix chain '4' and resid 403 through 409 removed outlier: 3.628A pdb=" N VAL 4 407 " --> pdb=" O VAL 4 403 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 13 removed outlier: 4.495A 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: 3.685A pdb=" N LEU 5 114 " --> pdb=" O SER 5 110 " (cutoff:3.500A) Processing helix chain '5' and resid 166 through 170 Processing helix chain '5' and resid 186 through 191 Processing helix chain '6' and resid 21 through 35 removed outlier: 3.564A pdb=" N SER 6 35 " --> pdb=" O GLY 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 53 removed outlier: 3.882A pdb=" N ILE 6 48 " --> pdb=" O ALA 6 44 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU 6 49 " --> pdb=" O CYS 6 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 6 53 " --> pdb=" O GLU 6 49 " (cutoff:3.500A) 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: 3.782A pdb=" N LEU 6 147 " --> pdb=" O ARG 6 143 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 19 removed outlier: 3.530A pdb=" N GLN 9 8 " --> pdb=" O LYS 9 4 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER 9 19 " --> pdb=" O LYS 9 15 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 63 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: 3.612A pdb=" N ARG 9 152 " --> pdb=" O ARG 9 148 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 28 removed outlier: 3.785A pdb=" N GLU 7 8 " --> pdb=" O SER 7 4 " (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 removed outlier: 3.605A pdb=" N GLY A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 84 Proline residue: A 80 - end of helix removed outlier: 3.786A pdb=" N SER A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 114 Processing helix chain 'J' and resid 2 through 22 removed outlier: 4.038A pdb=" N LEU J 7 " --> pdb=" O LEU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 46 Processing helix chain 'J' and resid 48 through 58 removed outlier: 3.649A pdb=" N GLY J 52 " --> pdb=" O ALA J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 74 Processing helix chain 'J' and resid 88 through 109 removed outlier: 3.920A pdb=" N LEU J 92 " --> pdb=" O ARG J 88 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 122 Processing helix chain 'J' and resid 123 through 132 removed outlier: 3.573A pdb=" N LEU J 127 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 135 through 158 Processing helix chain 'K' and resid 2 through 21 removed outlier: 3.760A pdb=" N ALA K 8 " --> pdb=" O LEU K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 50 removed outlier: 3.562A pdb=" N LEU K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA K 48 " --> pdb=" O GLY K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 80 removed outlier: 4.084A pdb=" N VAL K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 90 Processing helix chain 'L' and resid 2 through 20 removed outlier: 3.714A pdb=" N THR L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE L 7 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Proline residue: L 10 - end of helix removed outlier: 4.293A pdb=" N PHE L 14 " --> pdb=" O PRO L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 50 removed outlier: 3.506A pdb=" N SER L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU L 47 " --> pdb=" O LEU L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 95 removed outlier: 3.642A 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: 5.498A pdb=" N ALA L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG L 163 " --> pdb=" O PHE L 159 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY L 165 " --> pdb=" O VAL L 161 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU L 179 " --> pdb=" O ILE L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 193 Processing helix chain 'L' and resid 198 through 217 removed outlier: 3.514A pdb=" N GLY L 215 " --> pdb=" O LEU L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 231 Processing helix chain 'L' and resid 233 through 242 removed outlier: 3.771A pdb=" N SER L 237 " --> pdb=" O PRO L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 256 removed outlier: 3.840A pdb=" N GLY L 249 " --> pdb=" O MET L 245 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL L 250 " --> pdb=" O VAL L 246 " (cutoff:3.500A) removed outlier: 3.960A 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 285 removed outlier: 3.562A pdb=" N SER L 267 " --> pdb=" O LEU L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 310 removed outlier: 3.871A pdb=" N SER L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 342 removed outlier: 3.931A pdb=" N PHE L 327 " --> pdb=" O PHE L 323 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA L 330 " --> pdb=" O ALA L 326 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 338 " --> pdb=" O LEU L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 375 Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.959A pdb=" N LEU L 393 " --> pdb=" O LEU L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 426 removed outlier: 3.679A pdb=" N VAL L 404 " --> pdb=" O VAL L 400 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY L 405 " --> pdb=" O GLY L 401 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU L 408 " --> pdb=" O VAL L 404 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA L 417 " --> pdb=" O THR L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 456 removed outlier: 3.611A pdb=" N LEU L 443 " --> pdb=" O PRO L 439 " (cutoff:3.500A) Proline residue: L 445 - end of helix Processing helix chain 'L' and resid 469 through 474 Processing helix chain 'L' and resid 490 through 512 removed outlier: 3.919A pdb=" N GLY L 508 " --> pdb=" O GLY L 504 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE L 512 " --> pdb=" O GLY L 508 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 530 removed outlier: 3.713A pdb=" N ALA L 523 " --> pdb=" O ALA L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 542 removed outlier: 3.669A pdb=" N ALA L 537 " --> pdb=" O TYR L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 542 through 580 removed outlier: 3.511A pdb=" N GLU L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU L 567 " --> pdb=" O GLY L 563 " (cutoff:3.500A) Processing helix chain 'L' and resid 585 through 605 removed outlier: 3.748A pdb=" N ARG L 605 " --> pdb=" O LEU L 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 18 Proline residue: M 9 - end of helix removed outlier: 3.511A pdb=" N LEU M 16 " --> pdb=" O PHE M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 42 removed outlier: 3.646A pdb=" N VAL M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 60 Processing helix chain 'M' and resid 70 through 89 removed outlier: 4.047A pdb=" N PHE M 74 " --> pdb=" O LEU M 70 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 76 " --> pdb=" O ALA M 72 " (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: 4.165A 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: 4.446A pdb=" N ALA M 161 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA M 162 " --> pdb=" O PRO M 158 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'M' and resid 189 through 203 removed outlier: 4.042A 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: 3.592A pdb=" N ASN M 221 " --> pdb=" O PHE M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 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 276 removed outlier: 4.397A pdb=" N GLN M 255 " --> pdb=" O GLU M 251 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLY M 258 " --> pdb=" O ALA M 254 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU M 259 " --> pdb=" O GLN M 255 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 302 Processing helix chain 'M' and resid 304 through 337 removed outlier: 3.616A pdb=" N MET M 309 " --> pdb=" O PRO M 305 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU M 312 " --> pdb=" O ALA M 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 319 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU M 325 " --> pdb=" O TYR M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 367 Processing helix chain 'M' and resid 372 through 388 removed outlier: 4.450A pdb=" N GLY M 376 " --> pdb=" O SER M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 396 Processing helix chain 'M' and resid 397 through 415 removed outlier: 3.534A pdb=" N ALA M 401 " --> pdb=" O LEU M 397 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR M 413 " --> pdb=" O ALA M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 446 removed outlier: 3.868A pdb=" N GLY M 431 " --> pdb=" O GLY M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 447 through 450 Processing helix chain 'M' and resid 453 through 464 removed outlier: 4.412A pdb=" N LEU M 457 " --> pdb=" O GLY M 453 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 17 removed outlier: 3.951A pdb=" N LEU N 15 " --> pdb=" O VAL N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 43 Processing helix chain 'N' and resid 56 through 77 removed outlier: 3.575A pdb=" N VAL N 74 " --> pdb=" O ALA N 70 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 76 " --> pdb=" O TRP N 72 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL N 77 " --> pdb=" O THR N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 100 removed outlier: 5.220A 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: 3.560A pdb=" N ALA N 120 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 158 removed outlier: 3.575A pdb=" N GLU N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA N 133 " --> pdb=" O GLY N 129 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY N 156 " --> pdb=" O ALA N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 187 removed outlier: 3.670A pdb=" N ALA N 173 " --> pdb=" O GLY N 169 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU N 180 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL N 181 " --> pdb=" O GLY N 177 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY N 182 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 203 removed outlier: 4.275A pdb=" N ASP N 198 " --> pdb=" O PHE N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 225 removed outlier: 4.958A pdb=" N LYS N 216 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG N 225 " --> pdb=" O ALA N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 248 removed outlier: 3.626A pdb=" N ALA N 234 " --> pdb=" O PRO N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 273 removed outlier: 3.996A pdb=" N ALA N 266 " --> pdb=" O SER N 262 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU N 271 " --> pdb=" O GLY N 267 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA N 272 " --> pdb=" O TYR N 268 " (cutoff:3.500A) removed outlier: 3.995A 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 Processing helix chain 'N' and resid 319 through 335 Processing helix chain 'N' and resid 339 through 356 removed outlier: 4.032A pdb=" N TRP N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA N 348 " --> pdb=" O GLY N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 371 removed outlier: 3.523A pdb=" N VAL N 370 " --> pdb=" O VAL N 366 " (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: 3.815A pdb=" N ARG N 399 " --> pdb=" O PRO N 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 419 through 423 Processing helix chain 'H' and resid 9 through 43 removed outlier: 3.515A pdb=" N PHE H 42 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 67 Processing helix chain 'H' and resid 78 through 95 removed outlier: 3.515A pdb=" N VAL H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Proline residue: H 86 - end of helix removed outlier: 3.661A pdb=" N ALA H 93 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 144 removed outlier: 4.068A pdb=" N TYR H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA H 132 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY H 144 " --> pdb=" O GLY H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 178 removed outlier: 3.565A pdb=" N LEU H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY H 167 " --> pdb=" O GLU H 163 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU H 168 " --> pdb=" O LEU H 164 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU H 171 " --> pdb=" O GLY H 167 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA H 172 " --> pdb=" O LEU H 168 " (cutoff:3.500A) Proline residue: H 173 - end of helix removed outlier: 4.010A pdb=" N LEU H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 192 removed outlier: 3.515A pdb=" N GLU H 191 " --> pdb=" O ASN H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 212 Processing helix chain 'H' and resid 238 through 264 removed outlier: 3.896A pdb=" N ALA H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR H 249 " --> pdb=" O GLN H 245 " (cutoff:3.500A) Proline residue: H 260 - end of helix Processing helix chain 'H' and resid 276 through 297 removed outlier: 3.561A pdb=" N TRP H 297 " --> pdb=" O ILE H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 312 Processing helix chain 'H' and resid 312 through 330 Processing helix chain 'H' and resid 334 through 351 removed outlier: 4.000A pdb=" N LEU H 340 " --> pdb=" O TYR H 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 170 through 175 removed outlier: 3.559A pdb=" N VAL 1 134 " --> pdb=" O HIS 1 174 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR 1 88 " --> pdb=" O THR 1 217 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASN 1 219 " --> pdb=" O TYR 1 88 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE 1 90 " --> pdb=" O ASN 1 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 249 through 254 removed outlier: 3.692A pdb=" N TYR 1 252 " --> pdb=" O TYR 1 264 " (cutoff:3.500A) removed outlier: 3.601A 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: 6.886A pdb=" N ILE 1 331 " --> pdb=" O GLN 1 288 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE 1 290 " --> pdb=" O ILE 1 329 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE 1 329 " --> pdb=" O ILE 1 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 78 through 83 removed outlier: 3.513A pdb=" N SER 2 118 " --> pdb=" O TYR 2 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 2 82 " --> pdb=" O GLN 2 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 133 through 136 removed outlier: 3.757A pdb=" N ILE 2 134 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL 2 136 " --> pdb=" O PRO 2 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 9 through 11 Processing sheet with id=AA7, first strand: chain '3' and resid 168 through 171 removed outlier: 6.270A pdb=" N VAL 3 174 " --> pdb=" O LEU 3 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 201 through 202 removed outlier: 3.954A pdb=" N ASP 3 201 " --> pdb=" O GLY 3 212 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY 3 212 " --> pdb=" O ASP 3 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '3' and resid 250 through 255 removed outlier: 6.817A pdb=" N ARG 3 270 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU 3 274 " --> pdb=" O ARG 3 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 317 through 319 removed outlier: 6.450A pdb=" N VAL 3 583 " --> pdb=" O VAL 3 600 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU 3 602 " --> pdb=" O VAL 3 583 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET 3 585 " --> pdb=" O LEU 3 602 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY 3 342 " --> pdb=" O TYR 3 567 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 464 through 467 removed outlier: 4.501A pdb=" N ILE 3 464 " --> pdb=" O MET 3 448 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA 3 452 " --> pdb=" O GLU 3 466 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA 3 396 " --> pdb=" O ALA 3 449 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE 3 451 " --> pdb=" O ALA 3 396 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL 3 398 " --> pdb=" O PHE 3 451 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS 3 531 " --> pdb=" O PRO 3 503 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 612 through 615 Processing sheet with id=AB4, first strand: chain '3' and resid 733 through 738 removed outlier: 7.063A pdb=" N ALA 3 714 " --> pdb=" O ARG 3 746 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL 3 748 " --> pdb=" O ALA 3 714 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU 3 716 " --> pdb=" O VAL 3 748 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU 3 715 " --> pdb=" O SER 3 761 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR 3 693 " --> pdb=" O LEU 3 760 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA 3 762 " --> pdb=" O TYR 3 693 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG 3 695 " --> pdb=" O ALA 3 762 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 27 through 30 Processing sheet with id=AB6, first strand: chain '4' and resid 339 through 342 Processing sheet with id=AB7, first strand: chain '4' and resid 339 through 342 Processing sheet with id=AB8, first strand: chain '5' and resid 19 through 20 removed outlier: 3.700A pdb=" N ASN 5 24 " --> pdb=" O ASN 5 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '5' and resid 28 through 29 removed outlier: 4.206A pdb=" N TYR 5 93 " --> pdb=" O LEU 5 29 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE 5 68 " --> pdb=" O VAL 5 94 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA 5 69 " --> pdb=" O GLY 5 54 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY 5 54 " --> pdb=" O ALA 5 69 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL 5 71 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE 5 52 " --> pdb=" O VAL 5 71 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU 5 73 " --> pdb=" O ALA 5 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '5' and resid 157 through 158 Processing sheet with id=AC2, first strand: chain '6' and resid 38 through 42 removed outlier: 3.581A pdb=" N VAL 6 135 " --> pdb=" O VAL 6 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '9' and resid 31 through 32 removed outlier: 6.232A pdb=" N VAL 9 31 " --> pdb=" O VAL 9 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '9' and resid 39 through 43 removed outlier: 5.002A pdb=" N ARG 9 40 " --> pdb=" O GLY 9 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '9' and resid 68 through 74 removed outlier: 6.762A pdb=" N TYR 9 69 " --> pdb=" O TYR 9 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR 9 91 " --> pdb=" O TYR 9 69 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU 9 71 " --> pdb=" O LYS 9 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS 9 89 " --> pdb=" O GLU 9 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 30 through 36 removed outlier: 3.554A pdb=" N SER 7 60 " --> pdb=" O ARG 7 30 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR 7 56 " --> pdb=" O GLU 7 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP 7 36 " --> pdb=" O ILE 7 54 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE 7 54 " --> pdb=" O ASP 7 36 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N MET 7 55 " --> pdb=" O ASP 7 71 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP 7 71 " --> pdb=" O MET 7 55 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA 7 57 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU 7 69 " --> pdb=" O ALA 7 57 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU 7 59 " --> pdb=" O PHE 7 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE 7 91 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 53 through 58 Processing sheet with id=AC8, first strand: chain 'M' and resid 48 through 56 removed outlier: 7.048A pdb=" N ALA M 50 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU M 67 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN M 52 " --> pdb=" O PHE M 65 " (cutoff:3.500A) removed outlier: 7.672A 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: 3.716A pdb=" N VAL M 61 " --> pdb=" O LEU M 56 " (cutoff:3.500A) 1893 hydrogen bonds defined for protein. 5490 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: 7.81 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 18531 1.44 - 1.67: 18173 1.67 - 1.90: 256 1.90 - 2.13: 1 2.13 - 2.36: 91 Bond restraints: 37052 Sorted by residual: bond pdb=" CD GLU H 227 " pdb=" OE2 GLU H 227 " ideal model delta sigma weight residual 1.249 1.395 -0.146 1.90e-02 2.77e+03 5.93e+01 bond pdb=" CD GLU 9 92 " pdb=" OE1 GLU 9 92 " ideal model delta sigma weight residual 1.249 1.394 -0.145 1.90e-02 2.77e+03 5.86e+01 bond pdb=" CG ASP L 386 " pdb=" OD2 ASP L 386 " 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=" OE2 GLU A 110 " ideal model delta sigma weight residual 1.249 1.393 -0.144 1.90e-02 2.77e+03 5.78e+01 bond pdb=" CD GLU 3 415 " pdb=" OE2 GLU 3 415 " ideal model delta sigma weight residual 1.249 1.393 -0.144 1.90e-02 2.77e+03 5.74e+01 ... (remaining 37047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 40003 2.74 - 5.47: 8766 5.47 - 8.21: 1481 8.21 - 10.95: 191 10.95 - 13.69: 23 Bond angle restraints: 50464 Sorted by residual: angle pdb=" S1 FES 3 804 " pdb="FE2 FES 3 804 " pdb=" S2 FES 3 804 " ideal model delta sigma weight residual 104.33 117.80 -13.47 1.14e+00 7.69e-01 1.40e+02 angle pdb="FE1 FES 3 804 " pdb=" S2 FES 3 804 " pdb="FE2 FES 3 804 " ideal model delta sigma weight residual 75.66 63.13 12.53 1.14e+00 7.69e-01 1.21e+02 angle pdb="FE1 FES 3 804 " pdb=" S1 FES 3 804 " pdb="FE2 FES 3 804 " ideal model delta sigma weight residual 75.66 63.87 11.79 1.20e+00 6.94e-01 9.65e+01 angle pdb=" CA PRO M 215 " pdb=" C PRO M 215 " pdb=" N PRO M 216 " ideal model delta sigma weight residual 117.93 129.27 -11.34 1.20e+00 6.94e-01 8.94e+01 angle pdb=" CA PRO 4 337 " pdb=" C PRO 4 337 " pdb=" N PRO 4 338 " ideal model delta sigma weight residual 117.93 129.14 -11.21 1.20e+00 6.94e-01 8.72e+01 ... (remaining 50459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 20963 31.94 - 63.88: 564 63.88 - 95.82: 117 95.82 - 127.76: 0 127.76 - 159.69: 1 Dihedral angle restraints: 21645 sinusoidal: 8418 harmonic: 13227 Sorted by residual: dihedral pdb=" CA ALA 4 142 " pdb=" C ALA 4 142 " pdb=" N LEU 4 143 " pdb=" CA LEU 4 143 " ideal model delta harmonic sigma weight residual -180.00 -136.91 -43.09 0 5.00e+00 4.00e-02 7.43e+01 dihedral pdb=" CA ASP 6 55 " pdb=" C ASP 6 55 " pdb=" N ALA 6 56 " pdb=" CA ALA 6 56 " ideal model delta harmonic sigma weight residual 180.00 138.51 41.49 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA PHE H 219 " pdb=" C PHE H 219 " pdb=" N ASP H 220 " pdb=" CA ASP H 220 " ideal model delta harmonic sigma weight residual 180.00 139.60 40.40 0 5.00e+00 4.00e-02 6.53e+01 ... (remaining 21642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.193: 5636 4.193 - 8.386: 0 8.386 - 12.579: 0 12.579 - 16.771: 0 16.771 - 20.964: 28 Chirality restraints: 5664 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 10.41 -20.96 2.00e-01 2.50e+01 1.10e+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 10.40 -20.96 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE3 SF4 1 501 " pdb=" S1 SF4 1 501 " pdb=" S2 SF4 1 501 " pdb=" S4 SF4 1 501 " both_signs ideal model delta sigma weight residual False -10.55 10.12 -20.68 2.00e-01 2.50e+01 1.07e+04 ... (remaining 5661 not shown) Planarity restraints: 6374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 316 " -0.373 2.00e-02 2.50e+03 2.00e-01 7.98e+02 pdb=" CG TYR N 316 " 0.107 2.00e-02 2.50e+03 pdb=" CD1 TYR N 316 " 0.181 2.00e-02 2.50e+03 pdb=" CD2 TYR N 316 " 0.172 2.00e-02 2.50e+03 pdb=" CE1 TYR N 316 " 0.105 2.00e-02 2.50e+03 pdb=" CE2 TYR N 316 " 0.100 2.00e-02 2.50e+03 pdb=" CZ TYR N 316 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 316 " -0.292 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 4 257 " -0.256 2.00e-02 2.50e+03 1.39e-01 3.86e+02 pdb=" CG TYR 4 257 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR 4 257 " 0.102 2.00e-02 2.50e+03 pdb=" CD2 TYR 4 257 " 0.129 2.00e-02 2.50e+03 pdb=" CE1 TYR 4 257 " 0.077 2.00e-02 2.50e+03 pdb=" CE2 TYR 4 257 " 0.071 2.00e-02 2.50e+03 pdb=" CZ TYR 4 257 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR 4 257 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 344 " 0.258 2.00e-02 2.50e+03 1.36e-01 3.71e+02 pdb=" CG TYR M 344 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR M 344 " -0.117 2.00e-02 2.50e+03 pdb=" CD2 TYR M 344 " -0.117 2.00e-02 2.50e+03 pdb=" CE1 TYR M 344 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR M 344 " -0.070 2.00e-02 2.50e+03 pdb=" CZ TYR M 344 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR M 344 " 0.193 2.00e-02 2.50e+03 ... (remaining 6371 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1949 2.71 - 3.26: 37059 3.26 - 3.80: 57672 3.80 - 4.35: 73570 4.35 - 4.90: 121508 Nonbonded interactions: 291758 Sorted by model distance: nonbonded pdb=" O2P FMN 1 502 " pdb=" O4' FMN 1 502 " model vdw 2.162 3.040 nonbonded pdb=" CB ASN 1 220 " pdb=" O2P FMN 1 502 " model vdw 2.261 3.440 nonbonded pdb=" N SER H 179 " pdb=" O SER H 179 " model vdw 2.331 2.496 nonbonded pdb=" N ALA 5 173 " pdb=" O ALA 5 173 " model vdw 2.334 2.496 nonbonded pdb=" N MET 1 322 " pdb=" O MET 1 322 " model vdw 2.371 2.496 ... (remaining 291753 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: 12.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 35.360 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.023 1.422 37092 Z= 1.517 Angle : 2.404 57.023 50559 Z= 1.564 Chirality : 1.407 20.964 5664 Planarity : 0.023 0.204 6374 Dihedral : 15.365 159.694 13228 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 2.86 % Allowed : 9.56 % Favored : 87.58 % Rotamer: Outliers : 2.43 % Allowed : 6.43 % Favored : 91.14 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -3.11 (0.07), residues: 2460 sheet: -1.95 (0.28), residues: 291 loop : -3.27 (0.12), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 335 TYR 0.373 0.034 TYR N 316 PHE 0.141 0.021 PHE H 314 TRP 0.209 0.028 TRP M 213 HIS 0.010 0.002 HIS 4 93 Details of bonding type rmsd/Z covalent geometry : bond 0.02095 / 1.45 (37052) covalent geometry : angle 2.32955 / 1.56 (50464) SS BOND : bond 0.01700 / 0.89 ( 1) SS BOND : angle 40.35276 / 23.73 ( 2) hydrogen bonds : bond 0.24764 / 16.55 ( 1889) hydrogen bonds : angle 9.18796 / 6.42 ( 5490) metal coordination : bond 0.23749 / 19.49 ( 37) metal coordination : angle 12.72373 / 8.62 ( 93) Misc. bond : bond 0.57820 / 29.37 ( 2) *********************** 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 1431 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 1342 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 43 ARG cc_start: 0.7597 (mtm110) cc_final: 0.6794 (mtm110) REVERT: 1 79 MET cc_start: 0.8399 (mmm) cc_final: 0.7733 (mmm) REVERT: 1 189 MET cc_start: 0.7560 (mtm) cc_final: 0.7188 (mtm) REVERT: 1 238 PHE cc_start: 0.8426 (t80) cc_final: 0.7772 (t80) REVERT: 1 253 GLN cc_start: 0.7641 (mp10) cc_final: 0.7098 (pm20) REVERT: 1 385 GLU cc_start: 0.7939 (mt-10) cc_final: 0.5764 (mt-10) REVERT: 1 408 TRP cc_start: 0.8249 (m-10) cc_final: 0.7890 (m-10) REVERT: 2 43 PRO cc_start: 0.9248 (OUTLIER) cc_final: 0.9023 (Cg_endo) REVERT: 2 81 GLN cc_start: 0.8367 (mt0) cc_final: 0.8063 (mt0) REVERT: 2 141 TYR cc_start: 0.6911 (m-80) cc_final: 0.6607 (m-10) REVERT: 3 1 MET cc_start: 0.8294 (mtt) cc_final: 0.7953 (mtt) REVERT: 3 96 LEU cc_start: 0.8969 (mt) cc_final: 0.8675 (mt) REVERT: 3 133 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8646 (mmp80) REVERT: 3 214 MET cc_start: 0.7965 (tpt) cc_final: 0.6768 (tpt) REVERT: 3 239 THR cc_start: 0.8519 (m) cc_final: 0.7753 (t) REVERT: 3 274 LEU cc_start: 0.8990 (tp) cc_final: 0.8668 (tt) REVERT: 3 288 ILE cc_start: 0.8998 (pt) cc_final: 0.8671 (mt) REVERT: 3 391 LEU cc_start: 0.8889 (mt) cc_final: 0.8624 (mp) REVERT: 3 395 PHE cc_start: 0.8850 (t80) cc_final: 0.8284 (t80) REVERT: 3 494 LYS cc_start: 0.8558 (tttt) cc_final: 0.8281 (ttpp) REVERT: 3 582 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6311 (t80) REVERT: 3 618 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7185 (tt0) REVERT: 4 68 LYS cc_start: 0.9600 (tptt) cc_final: 0.9126 (tptp) REVERT: 4 93 HIS cc_start: 0.8801 (m90) cc_final: 0.8256 (m-70) REVERT: 4 94 ASP cc_start: 0.8527 (m-30) cc_final: 0.8105 (m-30) REVERT: 4 140 LEU cc_start: 0.8154 (tp) cc_final: 0.7132 (tt) REVERT: 4 160 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8771 (t80) REVERT: 4 184 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: 4 192 LYS cc_start: 0.8607 (mttt) cc_final: 0.8230 (mtmm) REVERT: 4 216 GLU cc_start: 0.5572 (mt-10) cc_final: 0.4879 (mt-10) REVERT: 4 268 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: 4 275 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7859 (mpp80) REVERT: 4 276 MET cc_start: 0.8955 (mmt) cc_final: 0.8544 (tpp) REVERT: 4 283 MET cc_start: 0.8063 (mtp) cc_final: 0.7846 (mtt) REVERT: 4 285 GLU cc_start: 0.6574 (tt0) cc_final: 0.6171 (tp30) REVERT: 4 309 ILE cc_start: 0.9375 (pt) cc_final: 0.9140 (pt) REVERT: 4 344 VAL cc_start: 0.9460 (t) cc_final: 0.9054 (p) REVERT: 4 396 ILE cc_start: 0.9224 (mt) cc_final: 0.8746 (tt) REVERT: 5 17 ILE cc_start: 0.8745 (mm) cc_final: 0.8318 (pt) REVERT: 5 22 LEU cc_start: 0.8983 (mm) cc_final: 0.8621 (mt) REVERT: 5 115 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: 5 146 LEU cc_start: 0.9351 (mt) cc_final: 0.8938 (mt) REVERT: 5 170 PHE cc_start: 0.6825 (m-80) cc_final: 0.6589 (m-80) REVERT: 5 177 LYS cc_start: 0.8799 (mttt) cc_final: 0.8561 (mttt) REVERT: 6 45 CYS cc_start: 0.9718 (OUTLIER) cc_final: 0.9311 (p) REVERT: 6 59 ASP cc_start: 0.7121 (m-30) cc_final: 0.5961 (m-30) REVERT: 6 78 MET cc_start: 0.9264 (ttm) cc_final: 0.9002 (ttm) REVERT: 6 88 MET cc_start: 0.9041 (tpt) cc_final: 0.8710 (tpt) REVERT: 6 101 ASP cc_start: 0.8278 (t70) cc_final: 0.7692 (t0) REVERT: 6 106 ILE cc_start: 0.9531 (mt) cc_final: 0.9243 (pt) REVERT: 6 108 MET cc_start: 0.9076 (ttt) cc_final: 0.8725 (ttm) REVERT: 6 114 SER cc_start: 0.9253 (m) cc_final: 0.8771 (p) REVERT: 6 125 GLN cc_start: 0.8307 (mt0) cc_final: 0.8105 (mt0) REVERT: 6 134 ASP cc_start: 0.9489 (m-30) cc_final: 0.9221 (m-30) REVERT: 6 157 LYS cc_start: 0.8839 (tttm) cc_final: 0.8625 (tttt) REVERT: 9 44 THR cc_start: 0.9500 (p) cc_final: 0.9173 (p) REVERT: 9 89 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8451 (tttm) REVERT: 9 114 VAL cc_start: 0.9205 (t) cc_final: 0.9003 (p) REVERT: 9 118 ASP cc_start: 0.9196 (m-30) cc_final: 0.8790 (m-30) REVERT: 9 119 PHE cc_start: 0.8890 (p90) cc_final: 0.8262 (p90) REVERT: 9 128 ASP cc_start: 0.8574 (m-30) cc_final: 0.8264 (m-30) REVERT: 9 131 TYR cc_start: 0.8481 (m-80) cc_final: 0.8116 (m-80) REVERT: 9 136 MET cc_start: 0.8748 (mtm) cc_final: 0.8382 (mtt) REVERT: 9 159 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8223 (m) REVERT: 9 170 LEU cc_start: 0.8877 (mt) cc_final: 0.8671 (mt) REVERT: 7 17 LEU cc_start: 0.8911 (mt) cc_final: 0.8681 (tp) REVERT: 7 91 ILE cc_start: 0.8754 (mt) cc_final: 0.8473 (tp) REVERT: 7 97 TYR cc_start: 0.7440 (t80) cc_final: 0.6979 (t80) REVERT: A 11 LEU cc_start: 0.8788 (mt) cc_final: 0.8511 (tt) REVERT: A 56 ARG cc_start: 0.7364 (mpt180) cc_final: 0.6948 (ptp-170) REVERT: A 57 PHE cc_start: 0.8601 (m-80) cc_final: 0.8164 (m-80) REVERT: A 72 ASP cc_start: 0.8035 (t70) cc_final: 0.7764 (t70) REVERT: A 104 PHE cc_start: 0.8710 (t80) cc_final: 0.8425 (t80) REVERT: A 108 LEU cc_start: 0.9066 (mt) cc_final: 0.8416 (tt) REVERT: A 110 GLU cc_start: 0.6848 (pp20) cc_final: 0.6128 (pp20) REVERT: J 20 VAL cc_start: 0.9017 (m) cc_final: 0.8718 (t) REVERT: J 36 PHE cc_start: 0.8909 (m-10) cc_final: 0.8355 (m-10) REVERT: J 55 GLN cc_start: 0.9192 (tp-100) cc_final: 0.8379 (tp40) REVERT: J 59 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7859 (t80) REVERT: J 64 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8153 (t) REVERT: J 65 VAL cc_start: 0.8196 (t) cc_final: 0.7984 (t) REVERT: J 67 PHE cc_start: 0.8190 (m-80) cc_final: 0.7930 (m-10) REVERT: J 139 LEU cc_start: 0.9545 (tp) cc_final: 0.9342 (tp) REVERT: J 140 LEU cc_start: 0.9181 (mt) cc_final: 0.8877 (mm) REVERT: K 19 LEU cc_start: 0.8643 (mt) cc_final: 0.8319 (mt) REVERT: K 28 PHE cc_start: 0.8094 (t80) cc_final: 0.6904 (t80) REVERT: K 36 ASN cc_start: 0.7977 (m110) cc_final: 0.6062 (m110) REVERT: K 80 ARG cc_start: 0.8294 (ttt90) cc_final: 0.8054 (ttp-110) REVERT: L 67 LEU cc_start: 0.8019 (mt) cc_final: 0.7763 (mt) REVERT: L 78 LEU cc_start: 0.8029 (mt) cc_final: 0.7821 (tp) REVERT: L 134 VAL cc_start: 0.7824 (m) cc_final: 0.7551 (t) REVERT: L 153 ASP cc_start: 0.8158 (m-30) cc_final: 0.7759 (t0) REVERT: L 169 PHE cc_start: 0.8045 (t80) cc_final: 0.7366 (t80) REVERT: L 187 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6857 (pp20) REVERT: L 188 LEU cc_start: 0.9275 (tp) cc_final: 0.8654 (tp) REVERT: L 192 MET cc_start: 0.8390 (ttm) cc_final: 0.8145 (mtp) REVERT: L 223 MET cc_start: 0.7177 (pp-130) cc_final: 0.6523 (pp-130) REVERT: L 244 THR cc_start: 0.7441 (p) cc_final: 0.6711 (p) REVERT: L 245 MET cc_start: 0.8316 (tpt) cc_final: 0.7064 (tpt) REVERT: L 261 SER cc_start: 0.8919 (p) cc_final: 0.8555 (m) REVERT: L 293 LYS cc_start: 0.8405 (mttm) cc_final: 0.7750 (mtpt) REVERT: L 334 LEU cc_start: 0.8115 (mt) cc_final: 0.7658 (mt) REVERT: L 463 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.5030 (t70) REVERT: L 483 HIS cc_start: 0.0532 (OUTLIER) cc_final: -0.0344 (p90) REVERT: M 67 LEU cc_start: 0.9213 (tp) cc_final: 0.8958 (tp) REVERT: M 106 LEU cc_start: 0.9134 (mt) cc_final: 0.8814 (mm) REVERT: M 107 LEU cc_start: 0.9078 (mt) cc_final: 0.8837 (mt) REVERT: M 116 LEU cc_start: 0.6310 (tp) cc_final: 0.5795 (tp) REVERT: M 132 MET cc_start: 0.8406 (ptm) cc_final: 0.7950 (ptp) REVERT: M 135 LEU cc_start: 0.8815 (mt) cc_final: 0.8516 (tp) REVERT: M 183 HIS cc_start: 0.7081 (m-70) cc_final: 0.6331 (m170) REVERT: M 201 PHE cc_start: 0.7975 (m-10) cc_final: 0.7741 (m-10) REVERT: M 251 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7019 (mp0) REVERT: M 386 LYS cc_start: 0.8173 (mttm) cc_final: 0.7770 (mttm) REVERT: M 435 LEU cc_start: 0.9259 (tp) cc_final: 0.8953 (tp) REVERT: N 119 TYR cc_start: 0.9341 (m-80) cc_final: 0.9055 (m-80) REVERT: N 163 LEU cc_start: 0.8107 (mt) cc_final: 0.7462 (mt) REVERT: N 210 PHE cc_start: 0.8082 (t80) cc_final: 0.7074 (t80) REVERT: N 214 SER cc_start: 0.9269 (m) cc_final: 0.9047 (p) REVERT: N 251 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8761 (mm-40) REVERT: N 345 LYS cc_start: 0.8991 (mttp) cc_final: 0.8615 (mttm) REVERT: H 56 LEU cc_start: 0.7540 (mt) cc_final: 0.6931 (tt) REVERT: H 64 ILE cc_start: 0.9252 (mt) cc_final: 0.9008 (tp) REVERT: H 65 LYS cc_start: 0.8921 (tttm) cc_final: 0.8651 (tttp) REVERT: H 79 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7011 (ttp80) REVERT: H 119 ASP cc_start: 0.7688 (m-30) cc_final: 0.7482 (m-30) REVERT: H 124 TYR cc_start: 0.8796 (t80) cc_final: 0.8368 (t80) REVERT: H 160 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8832 (tt) REVERT: H 166 LEU cc_start: 0.9101 (mt) cc_final: 0.8809 (tt) REVERT: H 186 VAL cc_start: 0.8786 (t) cc_final: 0.8204 (t) REVERT: H 225 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6283 (mt-10) REVERT: H 268 THR cc_start: 0.7269 (p) cc_final: 0.7029 (m) REVERT: H 277 LEU cc_start: 0.8938 (tp) cc_final: 0.8517 (mm) REVERT: H 303 ASP cc_start: 0.8501 (m-30) cc_final: 0.8105 (t0) REVERT: H 304 GLN cc_start: 0.8810 (mt0) cc_final: 0.8432 (mt0) outliers start: 89 outliers final: 27 residues processed: 1398 average time/residue: 0.2218 time to fit residues: 505.3827 Evaluate side-chains 866 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 825 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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: 10.0000 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 87 HIS 1 174 HIS 1 315 HIS ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 8 GLN 2 81 GLN 2 120 GLN ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 131 GLN 3 208 HIS 3 225 ASN 3 372 GLN 3 468 HIS 4 33 GLN 4 58 HIS 4 63 HIS 4 78 ASN 4 93 HIS 4 169 HIS 4 379 GLN 6 58 ASN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 150 GLN ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 433 HIS ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 HIS M 183 HIS N 245 ASN H 117 ASN ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS H 233 HIS H 304 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093390 restraints weight = 95849.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094894 restraints weight = 61955.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096815 restraints weight = 41392.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097005 restraints weight = 30758.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.097281 restraints weight = 26479.984| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.275 37092 Z= 0.430 Angle : 2.660 65.727 50559 Z= 1.503 Chirality : 0.441 6.498 5664 Planarity : 0.007 0.101 6374 Dihedral : 7.352 159.286 5088 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.81 % Favored : 93.78 % Rotamer: Outliers : 0.16 % Allowed : 4.18 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.11), residues: 4612 helix: -0.52 (0.09), residues: 2488 sheet: -1.64 (0.29), residues: 273 loop : -2.60 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 7 121 TYR 0.030 0.002 TYR M 119 PHE 0.033 0.002 PHE H 252 TRP 0.041 0.002 TRP A 79 HIS 0.021 0.002 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.43 (37052) covalent geometry : angle 2.31431 / 1.50 (50464) SS BOND : bond 0.00954 / 0.50 ( 1) SS BOND : angle 5.01843 / 2.70 ( 2) hydrogen bonds : bond 0.06383 / 4.30 ( 1889) hydrogen bonds : angle 5.59744 / 3.94 ( 5490) metal coordination : bond 0.04290 / 3.28 ( 37) metal coordination : angle 30.65773 / 21.69 ( 93) Misc. bond : bond 0.00722 / 0.35 ( 2) *********************** 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 1079 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1073 time to evaluate : 1.358 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: 1 79 MET cc_start: 0.8629 (mmm) cc_final: 0.8361 (mmm) REVERT: 1 103 ASP cc_start: 0.8513 (p0) cc_final: 0.8185 (m-30) REVERT: 1 189 MET cc_start: 0.7845 (mtm) cc_final: 0.7323 (mtm) REVERT: 1 208 GLN cc_start: 0.8205 (mt0) cc_final: 0.6942 (pp30) REVERT: 1 227 VAL cc_start: 0.8515 (t) cc_final: 0.8186 (p) REVERT: 1 268 MET cc_start: 0.7251 (mtm) cc_final: 0.6802 (mtp) REVERT: 1 311 MET cc_start: 0.8361 (mtm) cc_final: 0.8066 (mtm) REVERT: 1 338 VAL cc_start: 0.8303 (t) cc_final: 0.8092 (p) REVERT: 2 81 GLN cc_start: 0.8488 (mt0) cc_final: 0.7693 (mt0) REVERT: 2 141 TYR cc_start: 0.7317 (m-80) cc_final: 0.6866 (m-10) REVERT: 2 161 LYS cc_start: 0.7963 (mttm) cc_final: 0.7513 (mtpp) REVERT: 2 162 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6554 (ptp90) REVERT: 3 3 ARG cc_start: 0.7197 (mmp-170) cc_final: 0.6722 (mtp85) REVERT: 3 139 LEU cc_start: 0.7132 (tt) cc_final: 0.6791 (pp) REVERT: 3 205 ARG cc_start: 0.7378 (ptt180) cc_final: 0.7133 (ptt90) REVERT: 3 236 LEU cc_start: 0.8791 (mt) cc_final: 0.8545 (mt) REVERT: 3 239 THR cc_start: 0.8765 (m) cc_final: 0.7961 (t) REVERT: 3 249 MET cc_start: 0.8925 (mmt) cc_final: 0.8565 (mmm) REVERT: 3 251 GLU cc_start: 0.7310 (pm20) cc_final: 0.7041 (pm20) REVERT: 3 288 ILE cc_start: 0.8891 (pt) cc_final: 0.8598 (mt) REVERT: 3 307 LYS cc_start: 0.7533 (mttt) cc_final: 0.6811 (mttt) REVERT: 3 395 PHE cc_start: 0.8963 (t80) cc_final: 0.8551 (t80) REVERT: 3 490 VAL cc_start: 0.9588 (t) cc_final: 0.9318 (p) REVERT: 3 494 LYS cc_start: 0.8888 (tttt) cc_final: 0.8425 (ttpp) REVERT: 3 526 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7054 (tm-30) REVERT: 3 547 MET cc_start: 0.8709 (tpp) cc_final: 0.8455 (tpp) REVERT: 3 558 TRP cc_start: 0.6781 (p-90) cc_final: 0.6520 (p-90) REVERT: 3 721 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6726 (mm-30) REVERT: 3 737 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7745 (mp0) REVERT: 3 738 THR cc_start: 0.8584 (m) cc_final: 0.8290 (m) REVERT: 4 40 VAL cc_start: 0.8792 (t) cc_final: 0.8423 (t) REVERT: 4 90 SER cc_start: 0.8776 (p) cc_final: 0.8239 (t) REVERT: 4 93 HIS cc_start: 0.8729 (m-70) cc_final: 0.8154 (m-70) REVERT: 4 208 PHE cc_start: 0.7748 (m-10) cc_final: 0.7251 (m-10) REVERT: 4 216 GLU cc_start: 0.4715 (mt-10) cc_final: 0.4230 (mt-10) REVERT: 4 276 MET cc_start: 0.8881 (mmt) cc_final: 0.8424 (tpp) REVERT: 4 283 MET cc_start: 0.8241 (mtp) cc_final: 0.7949 (ttm) REVERT: 4 322 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7707 (mt-10) REVERT: 5 22 LEU cc_start: 0.8622 (mm) cc_final: 0.8273 (mt) REVERT: 5 48 PHE cc_start: 0.7419 (t80) cc_final: 0.6987 (t80) REVERT: 5 117 GLU cc_start: 0.8592 (tt0) cc_final: 0.8291 (tt0) REVERT: 5 146 LEU cc_start: 0.9290 (mt) cc_final: 0.9001 (tt) REVERT: 6 51 MET cc_start: 0.8883 (mtp) cc_final: 0.8036 (ttm) REVERT: 6 78 MET cc_start: 0.9228 (ttm) cc_final: 0.8729 (ttm) REVERT: 6 114 SER cc_start: 0.9039 (m) cc_final: 0.8559 (p) REVERT: 9 36 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8451 (mtt90) REVERT: 9 114 VAL cc_start: 0.9180 (t) cc_final: 0.8968 (p) REVERT: 9 119 PHE cc_start: 0.8789 (p90) cc_final: 0.8117 (p90) REVERT: 9 121 MET cc_start: 0.8395 (pmm) cc_final: 0.8175 (pmm) REVERT: 9 159 VAL cc_start: 0.7853 (m) cc_final: 0.7534 (m) REVERT: 7 17 LEU cc_start: 0.8693 (mt) cc_final: 0.8475 (tp) REVERT: A 11 LEU cc_start: 0.9002 (mt) cc_final: 0.8419 (tt) REVERT: A 13 TYR cc_start: 0.8115 (t80) cc_final: 0.7493 (t80) REVERT: A 56 ARG cc_start: 0.7367 (mpt180) cc_final: 0.7135 (mtm180) REVERT: A 57 PHE cc_start: 0.8559 (m-80) cc_final: 0.8083 (m-80) REVERT: A 104 PHE cc_start: 0.8639 (t80) cc_final: 0.8253 (t80) REVERT: A 116 MET cc_start: 0.8138 (ptm) cc_final: 0.7854 (ppp) REVERT: J 5 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6645 (tp30) REVERT: J 47 ASP cc_start: 0.7682 (t0) cc_final: 0.7384 (t0) REVERT: J 55 GLN cc_start: 0.8836 (tp-100) cc_final: 0.7899 (tp40) REVERT: J 57 ILE cc_start: 0.8513 (mt) cc_final: 0.8293 (tt) REVERT: J 74 LEU cc_start: 0.8587 (tp) cc_final: 0.8226 (tp) REVERT: J 103 ILE cc_start: 0.8418 (mm) cc_final: 0.7805 (mt) REVERT: J 142 VAL cc_start: 0.9140 (t) cc_final: 0.8864 (t) REVERT: K 30 SER cc_start: 0.9063 (m) cc_final: 0.8830 (p) REVERT: K 34 MET cc_start: 0.7843 (mtp) cc_final: 0.7591 (mtp) REVERT: K 70 VAL cc_start: 0.9465 (m) cc_final: 0.9139 (p) REVERT: L 87 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9131 (tt) REVERT: L 107 TYR cc_start: 0.8669 (m-80) cc_final: 0.8349 (m-10) REVERT: L 153 ASP cc_start: 0.8649 (m-30) cc_final: 0.7847 (t0) REVERT: L 169 PHE cc_start: 0.8766 (t80) cc_final: 0.8134 (t80) REVERT: L 170 MET cc_start: 0.8342 (mtm) cc_final: 0.8049 (mmm) REVERT: L 187 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7173 (pp20) REVERT: L 188 LEU cc_start: 0.9375 (tp) cc_final: 0.8889 (tp) REVERT: L 192 MET cc_start: 0.8502 (ttm) cc_final: 0.8031 (mtp) REVERT: L 219 GLN cc_start: 0.7675 (mp10) cc_final: 0.6933 (mp10) REVERT: L 223 MET cc_start: 0.7630 (ptt) cc_final: 0.7068 (ptp) REVERT: L 265 ASP cc_start: 0.7169 (p0) cc_final: 0.6921 (t0) REVERT: L 293 LYS cc_start: 0.7949 (mttm) cc_final: 0.7411 (tttt) REVERT: L 319 LEU cc_start: 0.9089 (mt) cc_final: 0.8765 (mm) REVERT: L 328 PHE cc_start: 0.8471 (p90) cc_final: 0.8164 (p90) REVERT: L 334 LEU cc_start: 0.8460 (mt) cc_final: 0.8008 (mt) REVERT: M 103 GLU cc_start: 0.8109 (tp30) cc_final: 0.7685 (tp30) REVERT: M 107 LEU cc_start: 0.9164 (mt) cc_final: 0.8619 (mt) REVERT: M 135 LEU cc_start: 0.9153 (mt) cc_final: 0.8600 (tp) REVERT: M 217 PHE cc_start: 0.9015 (t80) cc_final: 0.8806 (t80) REVERT: M 251 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6831 (mp0) REVERT: M 386 LYS cc_start: 0.8209 (mttm) cc_final: 0.7882 (tptp) REVERT: M 435 LEU cc_start: 0.9379 (tp) cc_final: 0.9170 (tp) REVERT: N 35 LEU cc_start: 0.9307 (tp) cc_final: 0.9017 (tp) REVERT: N 63 THR cc_start: 0.9358 (t) cc_final: 0.9145 (t) REVERT: N 71 LEU cc_start: 0.9286 (mt) cc_final: 0.9072 (mp) REVERT: N 79 SER cc_start: 0.8368 (m) cc_final: 0.8041 (t) REVERT: N 119 TYR cc_start: 0.9252 (m-80) cc_final: 0.9039 (m-80) REVERT: N 135 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8455 (mttp) REVERT: N 265 HIS cc_start: 0.8144 (m-70) cc_final: 0.7750 (m-70) REVERT: N 318 LYS cc_start: 0.7174 (mttt) cc_final: 0.6565 (mmtt) REVERT: N 345 LYS cc_start: 0.8529 (mttp) cc_final: 0.8296 (mttm) REVERT: H 56 LEU cc_start: 0.7524 (mt) cc_final: 0.6954 (tt) REVERT: H 64 ILE cc_start: 0.9159 (mt) cc_final: 0.8909 (tp) REVERT: H 79 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7312 (ttp-170) REVERT: H 124 TYR cc_start: 0.8786 (t80) cc_final: 0.8253 (t80) REVERT: H 146 LYS cc_start: 0.8987 (mptt) cc_final: 0.8656 (mmtt) REVERT: H 166 LEU cc_start: 0.8824 (mt) cc_final: 0.8557 (tt) REVERT: H 235 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7008 (mp0) REVERT: H 268 THR cc_start: 0.6545 (p) cc_final: 0.6192 (m) REVERT: H 277 LEU cc_start: 0.8545 (tp) cc_final: 0.8301 (mt) REVERT: H 304 GLN cc_start: 0.8513 (mt0) cc_final: 0.8250 (mt0) outliers start: 6 outliers final: 2 residues processed: 1077 average time/residue: 0.2067 time to fit residues: 370.1292 Evaluate side-chains 767 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 764 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 173 optimal weight: 4.9990 chunk 426 optimal weight: 9.9990 chunk 337 optimal weight: 8.9990 chunk 419 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 245 GLN 1 288 GLN ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 HIS 2 135 GLN 2 137 ASN ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 38 HIS 3 183 HIS 3 392 GLN 3 468 HIS ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 129 HIS 9 46 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN ** L 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 483 HIS ** L 582 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 = 0.3384 r_free = 0.3384 target = 0.102722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089942 restraints weight = 99040.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.091237 restraints weight = 61146.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.093034 restraints weight = 44444.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093306 restraints weight = 36606.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093480 restraints weight = 28985.350| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.267 37092 Z= 0.453 Angle : 2.669 67.787 50559 Z= 1.501 Chirality : 0.445 6.473 5664 Planarity : 0.007 0.106 6374 Dihedral : 7.013 160.619 5088 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Rotamer: Outliers : 0.14 % Allowed : 4.35 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.09 % 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: -1.33 (0.12), residues: 4612 helix: 0.27 (0.10), residues: 2475 sheet: -1.32 (0.28), residues: 312 loop : -2.46 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 69 TYR 0.036 0.003 TYR M 119 PHE 0.030 0.003 PHE 3 395 TRP 0.039 0.002 TRP A 79 HIS 0.012 0.002 HIS 9 41 Details of bonding type rmsd/Z covalent geometry : bond 0.01234 / 0.45 (37052) covalent geometry : angle 2.31601 / 1.50 (50464) SS BOND : bond 0.09075 / 4.78 ( 1) SS BOND : angle 4.55087 / 2.67 ( 2) hydrogen bonds : bond 0.05921 / 3.98 ( 1889) hydrogen bonds : angle 5.43296 / 3.82 ( 5490) metal coordination : bond 0.04485 / 3.40 ( 37) metal coordination : angle 31.01360 / 22.03 ( 93) Misc. bond : bond 0.01236 / 0.59 ( 2) *********************** 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 899 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 894 time to evaluate : 1.211 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: 1 189 MET cc_start: 0.7923 (mtm) cc_final: 0.7366 (mtm) REVERT: 1 227 VAL cc_start: 0.8739 (t) cc_final: 0.8263 (p) REVERT: 1 249 MET cc_start: 0.6709 (pmm) cc_final: 0.6495 (pmm) REVERT: 1 268 MET cc_start: 0.7137 (mtm) cc_final: 0.6764 (mtp) REVERT: 1 317 GLN cc_start: 0.8360 (tt0) cc_final: 0.8121 (pt0) REVERT: 1 367 MET cc_start: 0.9020 (mtp) cc_final: 0.8624 (mtt) REVERT: 2 89 LYS cc_start: 0.7587 (tptt) cc_final: 0.6951 (tppt) REVERT: 2 143 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8151 (mp0) REVERT: 2 161 LYS cc_start: 0.8031 (mttm) cc_final: 0.7480 (mtpp) REVERT: 3 249 MET cc_start: 0.8920 (mmt) cc_final: 0.8553 (mmm) REVERT: 3 288 ILE cc_start: 0.8684 (pt) cc_final: 0.8440 (mt) REVERT: 3 420 LEU cc_start: 0.8080 (tp) cc_final: 0.7846 (tp) REVERT: 3 494 LYS cc_start: 0.8897 (tttt) cc_final: 0.8403 (ttpp) REVERT: 3 547 MET cc_start: 0.8778 (tpp) cc_final: 0.8345 (tpp) REVERT: 3 558 TRP cc_start: 0.6726 (p-90) cc_final: 0.6287 (p-90) REVERT: 3 590 LEU cc_start: 0.7804 (mm) cc_final: 0.7547 (pp) REVERT: 3 640 VAL cc_start: 0.9143 (t) cc_final: 0.8927 (m) REVERT: 3 721 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6666 (mm-30) REVERT: 3 737 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7730 (mp0) REVERT: 3 738 THR cc_start: 0.8760 (m) cc_final: 0.8534 (m) REVERT: 4 40 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8689 (t) REVERT: 4 66 PHE cc_start: 0.9019 (m-80) cc_final: 0.8545 (m-80) REVERT: 4 80 THR cc_start: 0.9520 (p) cc_final: 0.9226 (t) REVERT: 4 90 SER cc_start: 0.8777 (p) cc_final: 0.8371 (t) REVERT: 4 130 LEU cc_start: 0.9275 (mm) cc_final: 0.8906 (mm) REVERT: 4 216 GLU cc_start: 0.4881 (mt-10) cc_final: 0.4639 (mt-10) REVERT: 4 276 MET cc_start: 0.9040 (mmt) cc_final: 0.8753 (tpp) REVERT: 4 385 CYS cc_start: 0.8051 (p) cc_final: 0.7517 (p) REVERT: 5 22 LEU cc_start: 0.8666 (mm) cc_final: 0.8383 (mt) REVERT: 6 51 MET cc_start: 0.8595 (mtp) cc_final: 0.7949 (ttm) REVERT: 6 78 MET cc_start: 0.8871 (ttm) cc_final: 0.8594 (ttm) REVERT: 6 99 MET cc_start: 0.9163 (mtm) cc_final: 0.8817 (ptp) REVERT: 6 103 LYS cc_start: 0.7962 (pttt) cc_final: 0.7340 (ptpt) REVERT: 6 108 MET cc_start: 0.9014 (ttt) cc_final: 0.8779 (ttt) REVERT: 6 114 SER cc_start: 0.9089 (m) cc_final: 0.8595 (p) REVERT: 9 95 MET cc_start: 0.8614 (mmm) cc_final: 0.8079 (mmm) REVERT: 9 119 PHE cc_start: 0.8769 (p90) cc_final: 0.8564 (p90) REVERT: 7 121 ARG cc_start: 0.8094 (mpp80) cc_final: 0.7515 (mpp80) REVERT: A 11 LEU cc_start: 0.8888 (mt) cc_final: 0.8295 (tt) REVERT: A 13 TYR cc_start: 0.8452 (t80) cc_final: 0.8247 (t80) REVERT: A 57 PHE cc_start: 0.8598 (m-80) cc_final: 0.8273 (m-80) REVERT: A 104 PHE cc_start: 0.8567 (t80) cc_final: 0.8264 (t80) REVERT: J 47 ASP cc_start: 0.8105 (t0) cc_final: 0.7901 (t0) REVERT: J 72 MET cc_start: 0.8242 (mtt) cc_final: 0.7915 (mtm) REVERT: J 103 ILE cc_start: 0.8379 (mm) cc_final: 0.8125 (mt) REVERT: J 136 LEU cc_start: 0.8484 (pt) cc_final: 0.7926 (tp) REVERT: J 142 VAL cc_start: 0.9127 (t) cc_final: 0.8879 (t) REVERT: K 15 VAL cc_start: 0.9483 (t) cc_final: 0.9263 (p) REVERT: K 34 MET cc_start: 0.8001 (mtp) cc_final: 0.7709 (mtp) REVERT: K 70 VAL cc_start: 0.9280 (m) cc_final: 0.8906 (p) REVERT: L 104 PHE cc_start: 0.9215 (t80) cc_final: 0.8962 (t80) REVERT: L 107 TYR cc_start: 0.8681 (m-80) cc_final: 0.8450 (m-10) REVERT: L 127 MET cc_start: 0.8831 (ttp) cc_final: 0.8595 (ptm) REVERT: L 153 ASP cc_start: 0.8614 (m-30) cc_final: 0.7989 (t0) REVERT: L 169 PHE cc_start: 0.8762 (t80) cc_final: 0.8342 (t80) REVERT: L 187 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7085 (pm20) REVERT: L 192 MET cc_start: 0.8693 (ttm) cc_final: 0.8362 (mtp) REVERT: L 219 GLN cc_start: 0.7707 (mp10) cc_final: 0.7219 (mp10) REVERT: L 223 MET cc_start: 0.8189 (ptt) cc_final: 0.7564 (ptp) REVERT: L 265 ASP cc_start: 0.7174 (p0) cc_final: 0.6826 (t0) REVERT: L 306 MET cc_start: 0.8433 (mmm) cc_final: 0.8148 (mmm) REVERT: L 319 LEU cc_start: 0.9260 (mt) cc_final: 0.8974 (mm) REVERT: L 328 PHE cc_start: 0.8515 (p90) cc_final: 0.8142 (p90) REVERT: L 334 LEU cc_start: 0.8293 (mt) cc_final: 0.7888 (mt) REVERT: L 412 LEU cc_start: 0.8532 (mt) cc_final: 0.8255 (mt) REVERT: L 416 TYR cc_start: 0.8381 (p90) cc_final: 0.7956 (p90) REVERT: M 135 LEU cc_start: 0.9226 (mt) cc_final: 0.8527 (tp) REVERT: M 435 LEU cc_start: 0.9392 (tp) cc_final: 0.9178 (tp) REVERT: M 457 LEU cc_start: 0.8352 (mm) cc_final: 0.7927 (mm) REVERT: N 63 THR cc_start: 0.9436 (t) cc_final: 0.9110 (t) REVERT: N 135 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8775 (mttp) REVERT: N 261 SER cc_start: 0.9445 (m) cc_final: 0.9061 (p) REVERT: N 265 HIS cc_start: 0.7686 (m-70) cc_final: 0.6871 (m-70) REVERT: N 301 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7637 (tp-100) REVERT: N 318 LYS cc_start: 0.7471 (mttt) cc_final: 0.6842 (mmtt) REVERT: N 345 LYS cc_start: 0.8874 (mttp) cc_final: 0.8525 (mttm) REVERT: H 31 MET cc_start: 0.7032 (tmm) cc_final: 0.6634 (ttp) REVERT: H 79 ARG cc_start: 0.7989 (mmt180) cc_final: 0.7207 (ttp-170) REVERT: H 84 LEU cc_start: 0.9333 (tp) cc_final: 0.9125 (tp) REVERT: H 137 PHE cc_start: 0.7974 (p90) cc_final: 0.7470 (p90) REVERT: H 146 LYS cc_start: 0.8862 (mptt) cc_final: 0.8628 (mmtt) REVERT: H 148 SER cc_start: 0.7589 (m) cc_final: 0.7326 (t) REVERT: H 186 VAL cc_start: 0.8858 (t) cc_final: 0.8424 (t) REVERT: H 189 GLN cc_start: 0.8600 (mp10) cc_final: 0.8189 (mp10) REVERT: H 235 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7700 (mp0) REVERT: H 277 LEU cc_start: 0.8491 (tp) cc_final: 0.8184 (mm) REVERT: H 304 GLN cc_start: 0.8164 (mt0) cc_final: 0.7920 (mt0) REVERT: H 328 VAL cc_start: 0.8570 (t) cc_final: 0.8318 (t) outliers start: 5 outliers final: 0 residues processed: 895 average time/residue: 0.2088 time to fit residues: 314.1866 Evaluate side-chains 687 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 686 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 428 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 431 optimal weight: 0.0370 chunk 182 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 402 optimal weight: 7.9990 chunk 331 optimal weight: 9.9990 chunk 271 optimal weight: 0.9990 chunk 133 optimal weight: 0.4980 overall best weight: 1.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 87 HIS ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 591 HIS 4 377 ASN 4 379 GLN 5 112 ASN J 24 ASN J 55 GLN ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 347 GLN ** L 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 582 GLN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN H 183 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094088 restraints weight = 95245.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096168 restraints weight = 63404.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097852 restraints weight = 38910.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098012 restraints weight = 30872.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098190 restraints weight = 26508.522| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.264 37092 Z= 0.401 Angle : 2.614 66.126 50559 Z= 1.477 Chirality : 0.445 6.600 5664 Planarity : 0.006 0.111 6374 Dihedral : 6.522 166.226 5088 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.90 % Favored : 94.84 % Rotamer: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.75 % 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: -0.78 (0.12), residues: 4612 helix: 0.76 (0.10), residues: 2484 sheet: -1.25 (0.28), residues: 314 loop : -2.23 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 6 69 TYR 0.039 0.002 TYR M 119 PHE 0.032 0.002 PHE H 30 TRP 0.054 0.002 TRP A 79 HIS 0.021 0.001 HIS 2 177 Details of bonding type rmsd/Z covalent geometry : bond 0.01162 / 0.40 (37052) covalent geometry : angle 2.25933 / 1.47 (50464) SS BOND : bond 0.00501 / 0.26 ( 1) SS BOND : angle 3.09154 / 1.78 ( 2) hydrogen bonds : bond 0.04904 / 3.31 ( 1889) hydrogen bonds : angle 4.90976 / 3.44 ( 5490) metal coordination : bond 0.03400 / 2.61 ( 37) metal coordination : angle 30.73441 / 21.77 ( 93) Misc. bond : bond 0.00489 / 0.24 ( 2) *********************** 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 973 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 968 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 125 ILE cc_start: 0.8246 (mp) cc_final: 0.7821 (mp) REVERT: 1 208 GLN cc_start: 0.8125 (mt0) cc_final: 0.7915 (mt0) REVERT: 1 238 PHE cc_start: 0.8286 (t80) cc_final: 0.7671 (t80) REVERT: 1 308 ASP cc_start: 0.7789 (m-30) cc_final: 0.7383 (p0) REVERT: 1 317 GLN cc_start: 0.8365 (tt0) cc_final: 0.8154 (pt0) REVERT: 1 367 MET cc_start: 0.8749 (mtp) cc_final: 0.8419 (mtt) REVERT: 2 78 TYR cc_start: 0.8219 (m-10) cc_final: 0.7883 (m-10) REVERT: 2 89 LYS cc_start: 0.7514 (tptt) cc_final: 0.6854 (tppt) REVERT: 2 161 LYS cc_start: 0.8151 (mttm) cc_final: 0.7599 (mtpp) REVERT: 3 132 ASP cc_start: 0.9284 (m-30) cc_final: 0.9069 (m-30) REVERT: 3 236 LEU cc_start: 0.8538 (mt) cc_final: 0.8306 (mt) REVERT: 3 249 MET cc_start: 0.8946 (mmt) cc_final: 0.8565 (mmm) REVERT: 3 490 VAL cc_start: 0.9577 (t) cc_final: 0.9220 (p) REVERT: 3 547 MET cc_start: 0.8663 (tpp) cc_final: 0.8290 (tpp) REVERT: 3 558 TRP cc_start: 0.6540 (p-90) cc_final: 0.6274 (p-90) REVERT: 3 603 PRO cc_start: 0.6847 (Cg_endo) cc_final: 0.6645 (Cg_exo) REVERT: 3 640 VAL cc_start: 0.8927 (t) cc_final: 0.8721 (m) REVERT: 3 721 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7461 (mm-30) REVERT: 4 90 SER cc_start: 0.8697 (p) cc_final: 0.8165 (t) REVERT: 4 130 LEU cc_start: 0.9290 (mm) cc_final: 0.8949 (mm) REVERT: 4 276 MET cc_start: 0.8700 (mmt) cc_final: 0.8346 (tpp) REVERT: 4 385 CYS cc_start: 0.7889 (p) cc_final: 0.7511 (t) REVERT: 4 393 MET cc_start: 0.8148 (tpt) cc_final: 0.7349 (tpt) REVERT: 5 3 LEU cc_start: 0.8235 (tt) cc_final: 0.7974 (mp) REVERT: 5 19 ASP cc_start: 0.8258 (t0) cc_final: 0.8051 (t0) REVERT: 5 48 PHE cc_start: 0.7659 (t80) cc_final: 0.7268 (t80) REVERT: 5 115 GLU cc_start: 0.8801 (tp30) cc_final: 0.8560 (tp30) REVERT: 6 99 MET cc_start: 0.8919 (mtm) cc_final: 0.8699 (mtm) REVERT: 6 108 MET cc_start: 0.9044 (ttt) cc_final: 0.8792 (ttt) REVERT: 6 113 SER cc_start: 0.9360 (m) cc_final: 0.9038 (p) REVERT: 6 114 SER cc_start: 0.8956 (m) cc_final: 0.8668 (p) REVERT: 6 170 LEU cc_start: 0.9111 (mm) cc_final: 0.8909 (mm) REVERT: 9 90 VAL cc_start: 0.8933 (t) cc_final: 0.8715 (t) REVERT: 9 119 PHE cc_start: 0.8753 (p90) cc_final: 0.8300 (p90) REVERT: 9 121 MET cc_start: 0.8473 (pmm) cc_final: 0.8130 (pmm) REVERT: 7 105 THR cc_start: 0.7548 (m) cc_final: 0.6664 (p) REVERT: 7 116 PHE cc_start: 0.8577 (m-10) cc_final: 0.8196 (m-10) REVERT: A 11 LEU cc_start: 0.8885 (mt) cc_final: 0.8228 (tt) REVERT: A 57 PHE cc_start: 0.8554 (m-80) cc_final: 0.8223 (m-80) REVERT: A 72 ASP cc_start: 0.8151 (t70) cc_final: 0.7847 (t70) REVERT: A 81 TYR cc_start: 0.8451 (t80) cc_final: 0.7963 (t80) REVERT: A 104 PHE cc_start: 0.8473 (t80) cc_final: 0.8193 (t80) REVERT: J 47 ASP cc_start: 0.8451 (t0) cc_final: 0.7708 (t0) REVERT: J 103 ILE cc_start: 0.8329 (mm) cc_final: 0.8065 (mt) REVERT: J 119 LEU cc_start: 0.9287 (mt) cc_final: 0.8809 (mp) REVERT: J 136 LEU cc_start: 0.8335 (pt) cc_final: 0.7891 (tp) REVERT: K 34 MET cc_start: 0.8362 (mtp) cc_final: 0.8028 (mtp) REVERT: K 39 ASN cc_start: 0.8779 (t0) cc_final: 0.8179 (t0) REVERT: K 43 VAL cc_start: 0.9386 (t) cc_final: 0.8971 (t) REVERT: K 70 VAL cc_start: 0.9141 (m) cc_final: 0.8816 (p) REVERT: L 22 LYS cc_start: 0.6935 (ptpp) cc_final: 0.6452 (mttt) REVERT: L 79 ILE cc_start: 0.8811 (mt) cc_final: 0.8595 (mt) REVERT: L 104 PHE cc_start: 0.9148 (t80) cc_final: 0.8773 (t80) REVERT: L 107 TYR cc_start: 0.8621 (m-80) cc_final: 0.8254 (m-10) REVERT: L 153 ASP cc_start: 0.8589 (m-30) cc_final: 0.7903 (t0) REVERT: L 187 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6819 (pm20) REVERT: L 192 MET cc_start: 0.8422 (ttm) cc_final: 0.8147 (mtp) REVERT: L 219 GLN cc_start: 0.7286 (mp10) cc_final: 0.6986 (mp10) REVERT: L 223 MET cc_start: 0.8057 (ptt) cc_final: 0.7373 (ptp) REVERT: L 265 ASP cc_start: 0.7189 (p0) cc_final: 0.6909 (t0) REVERT: L 293 LYS cc_start: 0.7927 (mttm) cc_final: 0.7317 (tttt) REVERT: L 328 PHE cc_start: 0.8379 (p90) cc_final: 0.7963 (p90) REVERT: L 334 LEU cc_start: 0.8241 (mt) cc_final: 0.7923 (mt) REVERT: L 373 LEU cc_start: 0.7428 (tp) cc_final: 0.6742 (pp) REVERT: L 412 LEU cc_start: 0.8385 (mt) cc_final: 0.7993 (mt) REVERT: L 416 TYR cc_start: 0.8346 (p90) cc_final: 0.7909 (p90) REVERT: L 449 LEU cc_start: 0.8342 (tp) cc_final: 0.8004 (tp) REVERT: M 122 PHE cc_start: 0.8897 (t80) cc_final: 0.8657 (t80) REVERT: M 132 MET cc_start: 0.9068 (ptm) cc_final: 0.8672 (ptp) REVERT: M 135 LEU cc_start: 0.9245 (mt) cc_final: 0.8607 (tp) REVERT: M 244 PHE cc_start: 0.7962 (m-80) cc_final: 0.7159 (m-10) REVERT: M 251 GLU cc_start: 0.7635 (mp0) cc_final: 0.6678 (tp30) REVERT: M 434 LEU cc_start: 0.9042 (mm) cc_final: 0.8643 (pp) REVERT: M 457 LEU cc_start: 0.8590 (mm) cc_final: 0.8301 (mm) REVERT: N 63 THR cc_start: 0.9396 (t) cc_final: 0.9171 (t) REVERT: N 135 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8688 (mttp) REVERT: N 261 SER cc_start: 0.9362 (m) cc_final: 0.9075 (p) REVERT: N 265 HIS cc_start: 0.7429 (m-70) cc_final: 0.6146 (m-70) REVERT: N 269 MET cc_start: 0.7772 (mpp) cc_final: 0.7383 (mpp) REVERT: N 318 LYS cc_start: 0.7362 (mttt) cc_final: 0.6760 (mmtt) REVERT: N 345 LYS cc_start: 0.8843 (mttp) cc_final: 0.8363 (mttm) REVERT: H 16 LYS cc_start: 0.6075 (tttp) cc_final: 0.5864 (tttp) REVERT: H 31 MET cc_start: 0.6970 (tmm) cc_final: 0.6684 (ttp) REVERT: H 54 PHE cc_start: 0.7306 (t80) cc_final: 0.6857 (t80) REVERT: H 64 ILE cc_start: 0.9351 (mt) cc_final: 0.9032 (tp) REVERT: H 79 ARG cc_start: 0.7956 (mmt180) cc_final: 0.7153 (ttp-170) REVERT: H 117 ASN cc_start: 0.7086 (OUTLIER) cc_final: 0.6824 (t0) REVERT: H 148 SER cc_start: 0.7080 (m) cc_final: 0.6790 (t) REVERT: H 186 VAL cc_start: 0.8993 (t) cc_final: 0.8390 (t) REVERT: H 189 GLN cc_start: 0.8698 (mp10) cc_final: 0.8035 (mp10) REVERT: H 235 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7769 (mp0) REVERT: H 273 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6430 (mm-30) REVERT: H 283 ILE cc_start: 0.9122 (mt) cc_final: 0.8794 (mt) REVERT: H 304 GLN cc_start: 0.8129 (mt0) cc_final: 0.7901 (mt0) REVERT: H 314 PHE cc_start: 0.8510 (t80) cc_final: 0.8221 (t80) outliers start: 5 outliers final: 1 residues processed: 969 average time/residue: 0.2064 time to fit residues: 335.4048 Evaluate side-chains 722 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 720 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 207 optimal weight: 30.0000 chunk 403 optimal weight: 6.9990 chunk 343 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 448 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 453 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 369 ASN ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 372 GLN 3 591 HIS 3 661 GLN ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 330 HIS 4 379 GLN ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091093 restraints weight = 97724.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092669 restraints weight = 62841.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094148 restraints weight = 43710.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094386 restraints weight = 36144.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094637 restraints weight = 30430.822| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.252 37092 Z= 0.425 Angle : 2.648 67.735 50559 Z= 1.487 Chirality : 0.444 6.512 5664 Planarity : 0.006 0.055 6374 Dihedral : 6.501 167.530 5088 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.03 % Favored : 93.69 % Rotamer: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % 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: -0.72 (0.12), residues: 4612 helix: 0.79 (0.10), residues: 2478 sheet: -1.26 (0.29), residues: 314 loop : -2.15 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 6 69 TYR 0.042 0.002 TYR M 119 PHE 0.032 0.002 PHE 4 160 TRP 0.047 0.002 TRP A 79 HIS 0.015 0.002 HIS 2 177 Details of bonding type rmsd/Z covalent geometry : bond 0.01193 / 0.42 (37052) covalent geometry : angle 2.28336 / 1.48 (50464) SS BOND : bond 0.00914 / 0.48 ( 1) SS BOND : angle 3.42565 / 1.93 ( 2) hydrogen bonds : bond 0.05057 / 3.43 ( 1889) hydrogen bonds : angle 5.01332 / 3.51 ( 5490) metal coordination : bond 0.03518 / 2.70 ( 37) metal coordination : angle 31.36966 / 22.01 ( 93) Misc. bond : bond 0.00434 / 0.21 ( 2) *********************** 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 854 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 853 time to evaluate : 1.240 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: 1 147 GLN cc_start: 0.8177 (tp40) cc_final: 0.7846 (tp40) REVERT: 1 191 SER cc_start: 0.9014 (m) cc_final: 0.8429 (m) REVERT: 1 238 PHE cc_start: 0.8229 (t80) cc_final: 0.7570 (t80) REVERT: 1 249 MET cc_start: 0.7097 (pmm) cc_final: 0.6828 (pmm) REVERT: 1 268 MET cc_start: 0.7174 (mtm) cc_final: 0.6067 (mpp) REVERT: 1 308 ASP cc_start: 0.7840 (m-30) cc_final: 0.7370 (p0) REVERT: 1 367 MET cc_start: 0.8814 (mtp) cc_final: 0.8441 (mtt) REVERT: 2 28 MET cc_start: 0.8099 (mtp) cc_final: 0.7648 (mtp) REVERT: 2 78 TYR cc_start: 0.8441 (m-10) cc_final: 0.7981 (m-10) REVERT: 2 89 LYS cc_start: 0.7611 (tptt) cc_final: 0.6931 (tppt) REVERT: 2 121 LYS cc_start: 0.8826 (mttm) cc_final: 0.8539 (mmtt) REVERT: 2 141 TYR cc_start: 0.7618 (m-80) cc_final: 0.6954 (m-10) REVERT: 2 161 LYS cc_start: 0.8254 (mttm) cc_final: 0.7703 (mtpp) REVERT: 3 132 ASP cc_start: 0.9060 (m-30) cc_final: 0.8839 (m-30) REVERT: 3 214 MET cc_start: 0.7170 (mmm) cc_final: 0.6922 (tpp) REVERT: 3 249 MET cc_start: 0.8903 (mmt) cc_final: 0.8589 (mmm) REVERT: 3 395 PHE cc_start: 0.8708 (t80) cc_final: 0.8407 (t80) REVERT: 3 426 TYR cc_start: 0.7334 (m-80) cc_final: 0.6671 (m-80) REVERT: 3 490 VAL cc_start: 0.9570 (t) cc_final: 0.9251 (p) REVERT: 3 547 MET cc_start: 0.8652 (tpp) cc_final: 0.8389 (tpp) REVERT: 3 558 TRP cc_start: 0.6482 (p-90) cc_final: 0.6127 (p-90) REVERT: 3 721 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6844 (mm-30) REVERT: 3 769 LEU cc_start: 0.8172 (mp) cc_final: 0.7655 (mp) REVERT: 4 130 LEU cc_start: 0.9367 (mm) cc_final: 0.8850 (mm) REVERT: 4 158 ASP cc_start: 0.9063 (m-30) cc_final: 0.8851 (m-30) REVERT: 4 159 LEU cc_start: 0.8959 (tt) cc_final: 0.8755 (tt) REVERT: 4 197 LEU cc_start: 0.9311 (mt) cc_final: 0.8921 (tt) REVERT: 4 385 CYS cc_start: 0.7876 (p) cc_final: 0.7507 (t) REVERT: 4 393 MET cc_start: 0.7965 (tpt) cc_final: 0.7163 (tpt) REVERT: 5 48 PHE cc_start: 0.7679 (t80) cc_final: 0.7317 (t80) REVERT: 6 62 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7672 (mtt90) REVERT: 6 103 LYS cc_start: 0.8558 (pttt) cc_final: 0.8174 (ptpp) REVERT: 6 114 SER cc_start: 0.8905 (m) cc_final: 0.8337 (p) REVERT: 9 34 LYS cc_start: 0.8896 (mptt) cc_final: 0.8679 (mptt) REVERT: 7 105 THR cc_start: 0.7819 (m) cc_final: 0.7250 (p) REVERT: A 11 LEU cc_start: 0.8808 (mt) cc_final: 0.8295 (tt) REVERT: A 57 PHE cc_start: 0.8590 (m-80) cc_final: 0.8234 (m-80) REVERT: A 66 MET cc_start: 0.8663 (tpp) cc_final: 0.8457 (tpp) REVERT: A 72 ASP cc_start: 0.8252 (t70) cc_final: 0.8039 (t70) REVERT: A 79 TRP cc_start: 0.8397 (m-90) cc_final: 0.8106 (m-90) REVERT: A 81 TYR cc_start: 0.8602 (t80) cc_final: 0.8042 (t80) REVERT: A 104 PHE cc_start: 0.8507 (t80) cc_final: 0.8268 (t80) REVERT: J 47 ASP cc_start: 0.8695 (t0) cc_final: 0.7979 (t0) REVERT: J 119 LEU cc_start: 0.9303 (mt) cc_final: 0.8957 (mt) REVERT: J 136 LEU cc_start: 0.8300 (pt) cc_final: 0.7805 (tp) REVERT: K 70 VAL cc_start: 0.9088 (m) cc_final: 0.8745 (p) REVERT: K 91 SER cc_start: 0.8388 (m) cc_final: 0.7783 (p) REVERT: L 78 LEU cc_start: 0.8602 (pp) cc_final: 0.8364 (mt) REVERT: L 104 PHE cc_start: 0.9139 (t80) cc_final: 0.8914 (t80) REVERT: L 107 TYR cc_start: 0.8748 (m-80) cc_final: 0.8231 (m-10) REVERT: L 111 PHE cc_start: 0.8484 (t80) cc_final: 0.8104 (t80) REVERT: L 127 MET cc_start: 0.8803 (ttp) cc_final: 0.8602 (ptp) REVERT: L 153 ASP cc_start: 0.8378 (m-30) cc_final: 0.8038 (t0) REVERT: L 169 PHE cc_start: 0.8842 (t80) cc_final: 0.8266 (t80) REVERT: L 187 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7049 (pm20) REVERT: L 192 MET cc_start: 0.8438 (ttm) cc_final: 0.8178 (mtp) REVERT: L 219 GLN cc_start: 0.7694 (mp10) cc_final: 0.7404 (mp10) REVERT: L 223 MET cc_start: 0.8233 (ptt) cc_final: 0.7545 (ptp) REVERT: L 244 THR cc_start: 0.7964 (p) cc_final: 0.7387 (p) REVERT: L 265 ASP cc_start: 0.6955 (p0) cc_final: 0.6633 (t0) REVERT: L 290 ASP cc_start: 0.8291 (m-30) cc_final: 0.8046 (m-30) REVERT: L 328 PHE cc_start: 0.8442 (p90) cc_final: 0.8118 (p90) REVERT: L 373 LEU cc_start: 0.7529 (tp) cc_final: 0.7093 (tp) REVERT: L 412 LEU cc_start: 0.8320 (mt) cc_final: 0.7923 (mt) REVERT: L 449 LEU cc_start: 0.8348 (tp) cc_final: 0.8142 (tp) REVERT: L 529 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7543 (tpm170) REVERT: M 7 LEU cc_start: 0.7453 (mp) cc_final: 0.7194 (mp) REVERT: M 122 PHE cc_start: 0.8835 (t80) cc_final: 0.8441 (t80) REVERT: M 132 MET cc_start: 0.9082 (ptm) cc_final: 0.8643 (ptp) REVERT: M 135 LEU cc_start: 0.9281 (mt) cc_final: 0.8600 (tp) REVERT: M 148 PHE cc_start: 0.9011 (t80) cc_final: 0.8651 (t80) REVERT: M 204 LYS cc_start: 0.8531 (tppt) cc_final: 0.8162 (tppp) REVERT: M 357 LEU cc_start: 0.9163 (tp) cc_final: 0.8946 (tp) REVERT: N 35 LEU cc_start: 0.9302 (tp) cc_final: 0.9079 (tp) REVERT: N 83 GLU cc_start: 0.8141 (mp0) cc_final: 0.7931 (mp0) REVERT: N 135 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8659 (mttp) REVERT: N 265 HIS cc_start: 0.7554 (m-70) cc_final: 0.6989 (m-70) REVERT: N 269 MET cc_start: 0.7980 (mpp) cc_final: 0.7597 (mpp) REVERT: N 318 LYS cc_start: 0.7166 (mttt) cc_final: 0.6688 (mmtt) REVERT: N 345 LYS cc_start: 0.9186 (mttp) cc_final: 0.8748 (mttm) REVERT: H 79 ARG cc_start: 0.7974 (mmt180) cc_final: 0.7169 (ttp-170) REVERT: H 170 LEU cc_start: 0.9261 (mm) cc_final: 0.8721 (tp) REVERT: H 186 VAL cc_start: 0.9009 (t) cc_final: 0.8507 (t) REVERT: H 189 GLN cc_start: 0.8612 (mp10) cc_final: 0.7940 (mp10) REVERT: H 273 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6889 (pm20) REVERT: H 314 PHE cc_start: 0.8729 (t80) cc_final: 0.7833 (t80) REVERT: H 328 VAL cc_start: 0.8740 (t) cc_final: 0.8476 (t) outliers start: 1 outliers final: 0 residues processed: 853 average time/residue: 0.2031 time to fit residues: 294.3404 Evaluate side-chains 662 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 203 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 chunk 162 optimal weight: 2.9990 chunk 434 optimal weight: 0.9980 chunk 382 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 342 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 369 ASN 1 420 GLN ** 2 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 465 HIS 3 591 HIS 3 616 ASN 3 719 HIS 3 733 GLN 4 166 GLN ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094762 restraints weight = 96891.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096231 restraints weight = 62624.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097917 restraints weight = 44277.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098307 restraints weight = 35475.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.098471 restraints weight = 28159.670| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.264 37092 Z= 0.400 Angle : 2.614 63.247 50559 Z= 1.476 Chirality : 0.442 6.440 5664 Planarity : 0.005 0.112 6374 Dihedral : 6.259 172.942 5088 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.66 % Favored : 95.06 % Rotamer: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.59 % 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: -0.47 (0.12), residues: 4612 helix: 0.98 (0.10), residues: 2462 sheet: -1.34 (0.28), residues: 305 loop : -1.96 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG M 22 TYR 0.039 0.002 TYR M 119 PHE 0.040 0.002 PHE 4 208 TRP 0.054 0.002 TRP A 79 HIS 0.014 0.001 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.40 (37052) covalent geometry : angle 2.25540 / 1.47 (50464) SS BOND : bond 0.00652 / 0.34 ( 1) SS BOND : angle 3.11666 / 1.77 ( 2) hydrogen bonds : bond 0.04579 / 3.10 ( 1889) hydrogen bonds : angle 4.79230 / 3.35 ( 5490) metal coordination : bond 0.03377 / 2.48 ( 37) metal coordination : angle 30.90623 / 21.60 ( 93) Misc. bond : bond 0.01108 / 0.53 ( 2) *********************** 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 903 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 901 time to evaluate : 1.292 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: 1 191 SER cc_start: 0.8899 (m) cc_final: 0.8447 (m) REVERT: 1 208 GLN cc_start: 0.8295 (mt0) cc_final: 0.7431 (pp30) REVERT: 1 227 VAL cc_start: 0.8432 (t) cc_final: 0.7908 (p) REVERT: 1 238 PHE cc_start: 0.8099 (t80) cc_final: 0.7523 (t80) REVERT: 1 249 MET cc_start: 0.6690 (pmm) cc_final: 0.6312 (pmm) REVERT: 1 268 MET cc_start: 0.6875 (mtm) cc_final: 0.6220 (mpp) REVERT: 1 308 ASP cc_start: 0.7495 (m-30) cc_final: 0.7233 (p0) REVERT: 1 367 MET cc_start: 0.8724 (mtp) cc_final: 0.8469 (mtt) REVERT: 2 28 MET cc_start: 0.7916 (mtp) cc_final: 0.7546 (mtp) REVERT: 2 71 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7972 (mt0) REVERT: 2 78 TYR cc_start: 0.8287 (m-10) cc_final: 0.7835 (m-10) REVERT: 2 89 LYS cc_start: 0.7549 (tptt) cc_final: 0.6698 (tppt) REVERT: 2 121 LYS cc_start: 0.8781 (mttm) cc_final: 0.8401 (mmtt) REVERT: 2 141 TYR cc_start: 0.7507 (m-80) cc_final: 0.7037 (m-10) REVERT: 2 161 LYS cc_start: 0.8144 (mttm) cc_final: 0.7860 (mmmm) REVERT: 3 132 ASP cc_start: 0.9105 (m-30) cc_final: 0.8801 (m-30) REVERT: 3 214 MET cc_start: 0.7276 (mmm) cc_final: 0.6875 (tpp) REVERT: 3 249 MET cc_start: 0.8870 (mmt) cc_final: 0.8585 (mmm) REVERT: 3 395 PHE cc_start: 0.8682 (t80) cc_final: 0.8365 (t80) REVERT: 3 490 VAL cc_start: 0.9546 (t) cc_final: 0.9181 (p) REVERT: 4 93 HIS cc_start: 0.8527 (m-70) cc_final: 0.7946 (m-70) REVERT: 4 130 LEU cc_start: 0.9378 (mm) cc_final: 0.8889 (mm) REVERT: 4 133 LEU cc_start: 0.8681 (tp) cc_final: 0.8437 (tp) REVERT: 4 159 LEU cc_start: 0.8888 (tt) cc_final: 0.8679 (tt) REVERT: 4 185 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6969 (mm-30) REVERT: 4 193 LEU cc_start: 0.9387 (tp) cc_final: 0.9004 (tp) REVERT: 4 197 LEU cc_start: 0.9291 (mt) cc_final: 0.8977 (tt) REVERT: 4 276 MET cc_start: 0.8499 (mmp) cc_final: 0.8299 (tpp) REVERT: 4 385 CYS cc_start: 0.7741 (p) cc_final: 0.7488 (t) REVERT: 4 393 MET cc_start: 0.7848 (tpt) cc_final: 0.7115 (tpt) REVERT: 5 48 PHE cc_start: 0.7424 (t80) cc_final: 0.7173 (t80) REVERT: 5 146 LEU cc_start: 0.9371 (mt) cc_final: 0.9110 (tt) REVERT: 6 103 LYS cc_start: 0.7910 (pttt) cc_final: 0.7502 (ptpp) REVERT: 6 114 SER cc_start: 0.9007 (m) cc_final: 0.8520 (p) REVERT: 6 134 ASP cc_start: 0.9214 (m-30) cc_final: 0.8861 (t0) REVERT: 9 95 MET cc_start: 0.8604 (mmm) cc_final: 0.8138 (mmm) REVERT: 9 135 ASP cc_start: 0.7963 (m-30) cc_final: 0.6896 (m-30) REVERT: 7 5 SER cc_start: 0.8158 (m) cc_final: 0.7744 (p) REVERT: 7 105 THR cc_start: 0.7675 (m) cc_final: 0.6978 (p) REVERT: 7 116 PHE cc_start: 0.8381 (m-10) cc_final: 0.8088 (m-10) REVERT: A 11 LEU cc_start: 0.8865 (mt) cc_final: 0.8164 (tt) REVERT: A 57 PHE cc_start: 0.8513 (m-80) cc_final: 0.8171 (m-80) REVERT: A 81 TYR cc_start: 0.8406 (t80) cc_final: 0.8009 (t80) REVERT: A 104 PHE cc_start: 0.8436 (t80) cc_final: 0.8206 (t80) REVERT: J 47 ASP cc_start: 0.8865 (t0) cc_final: 0.7880 (t0) REVERT: J 83 PHE cc_start: 0.4547 (m-80) cc_final: 0.3098 (p90) REVERT: J 119 LEU cc_start: 0.9215 (mt) cc_final: 0.8762 (mp) REVERT: J 136 LEU cc_start: 0.8119 (pt) cc_final: 0.7644 (tp) REVERT: K 15 VAL cc_start: 0.9428 (t) cc_final: 0.9207 (p) REVERT: K 70 VAL cc_start: 0.9017 (m) cc_final: 0.8639 (p) REVERT: L 78 LEU cc_start: 0.8226 (pp) cc_final: 0.8014 (mt) REVERT: L 104 PHE cc_start: 0.9047 (t80) cc_final: 0.8740 (t80) REVERT: L 107 TYR cc_start: 0.8641 (m-80) cc_final: 0.8196 (m-10) REVERT: L 126 VAL cc_start: 0.7440 (t) cc_final: 0.7235 (t) REVERT: L 153 ASP cc_start: 0.8322 (m-30) cc_final: 0.7970 (t0) REVERT: L 169 PHE cc_start: 0.8733 (t80) cc_final: 0.8231 (t80) REVERT: L 187 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7038 (pm20) REVERT: L 223 MET cc_start: 0.8037 (ptt) cc_final: 0.7308 (ptp) REVERT: L 265 ASP cc_start: 0.6912 (p0) cc_final: 0.6667 (t0) REVERT: L 373 LEU cc_start: 0.7455 (tp) cc_final: 0.6963 (pp) REVERT: L 412 LEU cc_start: 0.8467 (mt) cc_final: 0.8107 (mt) REVERT: L 416 TYR cc_start: 0.8334 (p90) cc_final: 0.8023 (p90) REVERT: L 449 LEU cc_start: 0.8134 (tp) cc_final: 0.7862 (tp) REVERT: L 529 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7260 (tpm170) REVERT: M 122 PHE cc_start: 0.8607 (t80) cc_final: 0.8380 (t80) REVERT: M 132 MET cc_start: 0.8975 (ptm) cc_final: 0.8530 (ptp) REVERT: M 135 LEU cc_start: 0.9302 (mt) cc_final: 0.8588 (tp) REVERT: M 204 LYS cc_start: 0.8488 (tppt) cc_final: 0.8071 (tppp) REVERT: M 434 LEU cc_start: 0.9067 (mm) cc_final: 0.8762 (pp) REVERT: N 35 LEU cc_start: 0.9246 (tp) cc_final: 0.9027 (tp) REVERT: N 135 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8604 (mttp) REVERT: N 251 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8807 (mm-40) REVERT: N 265 HIS cc_start: 0.7688 (m-70) cc_final: 0.6950 (m-70) REVERT: N 269 MET cc_start: 0.7854 (mpp) cc_final: 0.7597 (mpp) REVERT: N 318 LYS cc_start: 0.7087 (mttt) cc_final: 0.6641 (mmtt) REVERT: N 345 LYS cc_start: 0.9149 (mttp) cc_final: 0.8709 (mttm) REVERT: N 375 TYR cc_start: 0.9079 (m-10) cc_final: 0.8495 (m-10) REVERT: N 420 LEU cc_start: 0.8465 (tp) cc_final: 0.8130 (tt) REVERT: H 79 ARG cc_start: 0.7824 (mmt180) cc_final: 0.7137 (ttp-170) REVERT: H 170 LEU cc_start: 0.9111 (mm) cc_final: 0.8775 (tp) REVERT: H 181 ASN cc_start: 0.8382 (m-40) cc_final: 0.7969 (t0) REVERT: H 186 VAL cc_start: 0.8888 (t) cc_final: 0.8553 (t) REVERT: H 189 GLN cc_start: 0.8559 (mp10) cc_final: 0.7867 (mp10) REVERT: H 314 PHE cc_start: 0.8617 (t80) cc_final: 0.7709 (t80) outliers start: 2 outliers final: 0 residues processed: 901 average time/residue: 0.2001 time to fit residues: 304.6865 Evaluate side-chains 696 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 343 optimal weight: 9.9990 chunk 439 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 342 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 153 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 372 GLN 3 591 HIS 3 657 HIS 4 169 HIS 6 98 GLN ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN L 582 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN H 226 GLN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093099 restraints weight = 97857.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094452 restraints weight = 62696.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096091 restraints weight = 45368.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096480 restraints weight = 38393.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096592 restraints weight = 29511.049| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.260 37092 Z= 0.409 Angle : 2.627 66.662 50559 Z= 1.480 Chirality : 0.444 6.492 5664 Planarity : 0.005 0.062 6374 Dihedral : 6.286 174.591 5088 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.46 % Favored : 94.23 % Rotamer: Outliers : 0.03 % Allowed : 1.45 % Favored : 98.52 % 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: -0.50 (0.12), residues: 4612 helix: 0.97 (0.10), residues: 2467 sheet: -1.47 (0.28), residues: 321 loop : -1.97 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 6 62 TYR 0.036 0.002 TYR M 119 PHE 0.036 0.002 PHE 4 160 TRP 0.061 0.002 TRP A 79 HIS 0.013 0.001 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01173 / 0.41 (37052) covalent geometry : angle 2.26608 / 1.48 (50464) SS BOND : bond 0.00134 / 0.07 ( 1) SS BOND : angle 6.87425 / 3.13 ( 2) hydrogen bonds : bond 0.04609 / 3.13 ( 1889) hydrogen bonds : angle 4.82718 / 3.38 ( 5490) metal coordination : bond 0.03354 / 2.57 ( 37) metal coordination : angle 31.03704 / 21.47 ( 93) Misc. bond : bond 0.00738 / 0.35 ( 2) *********************** 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 862 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 861 time to evaluate : 1.052 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: 1 208 GLN cc_start: 0.8315 (mt0) cc_final: 0.7637 (mp10) REVERT: 1 227 VAL cc_start: 0.8409 (t) cc_final: 0.7876 (p) REVERT: 1 238 PHE cc_start: 0.8177 (t80) cc_final: 0.7552 (t80) REVERT: 1 308 ASP cc_start: 0.7523 (m-30) cc_final: 0.7272 (p0) REVERT: 1 367 MET cc_start: 0.8786 (mtp) cc_final: 0.8458 (mtt) REVERT: 2 28 MET cc_start: 0.7934 (mtp) cc_final: 0.7712 (mtp) REVERT: 2 78 TYR cc_start: 0.8406 (m-80) cc_final: 0.7783 (m-10) REVERT: 2 89 LYS cc_start: 0.7508 (tptt) cc_final: 0.6787 (tppt) REVERT: 2 141 TYR cc_start: 0.7662 (m-80) cc_final: 0.7149 (m-10) REVERT: 2 161 LYS cc_start: 0.8154 (mttm) cc_final: 0.7885 (mmmm) REVERT: 3 132 ASP cc_start: 0.9124 (m-30) cc_final: 0.8601 (m-30) REVERT: 3 249 MET cc_start: 0.8848 (mmt) cc_final: 0.8613 (mmm) REVERT: 3 395 PHE cc_start: 0.8739 (t80) cc_final: 0.8390 (t80) REVERT: 3 505 LEU cc_start: 0.7303 (tp) cc_final: 0.7068 (tp) REVERT: 3 558 TRP cc_start: 0.6736 (p-90) cc_final: 0.6533 (p-90) REVERT: 4 80 THR cc_start: 0.9545 (p) cc_final: 0.9280 (t) REVERT: 4 93 HIS cc_start: 0.8485 (m-70) cc_final: 0.8131 (m-70) REVERT: 4 130 LEU cc_start: 0.9497 (mm) cc_final: 0.9161 (mm) REVERT: 4 159 LEU cc_start: 0.8812 (tt) cc_final: 0.8603 (tt) REVERT: 4 185 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7206 (mm-30) REVERT: 4 197 LEU cc_start: 0.9308 (mt) cc_final: 0.9021 (tt) REVERT: 4 385 CYS cc_start: 0.7645 (p) cc_final: 0.7407 (t) REVERT: 4 393 MET cc_start: 0.7947 (tpt) cc_final: 0.7198 (tpt) REVERT: 5 13 LYS cc_start: 0.7887 (mttt) cc_final: 0.7602 (mtmt) REVERT: 5 48 PHE cc_start: 0.7436 (t80) cc_final: 0.7214 (t80) REVERT: 5 146 LEU cc_start: 0.9408 (mt) cc_final: 0.9152 (tt) REVERT: 5 185 LYS cc_start: 0.8647 (pttt) cc_final: 0.8226 (pttt) REVERT: 6 99 MET cc_start: 0.8399 (mtp) cc_final: 0.8135 (mtp) REVERT: 6 103 LYS cc_start: 0.8356 (pttt) cc_final: 0.8067 (ptpp) REVERT: 6 114 SER cc_start: 0.8917 (m) cc_final: 0.8346 (p) REVERT: 9 90 VAL cc_start: 0.8949 (t) cc_final: 0.8744 (t) REVERT: 9 135 ASP cc_start: 0.7632 (m-30) cc_final: 0.7242 (t0) REVERT: 7 5 SER cc_start: 0.7598 (m) cc_final: 0.6878 (p) REVERT: 7 116 PHE cc_start: 0.8394 (m-10) cc_final: 0.8066 (m-10) REVERT: A 11 LEU cc_start: 0.8745 (mt) cc_final: 0.8103 (tt) REVERT: A 57 PHE cc_start: 0.8413 (m-80) cc_final: 0.8018 (m-80) REVERT: A 81 TYR cc_start: 0.8503 (t80) cc_final: 0.8100 (t80) REVERT: A 104 PHE cc_start: 0.8367 (t80) cc_final: 0.8142 (t80) REVERT: J 47 ASP cc_start: 0.8695 (t0) cc_final: 0.7606 (t0) REVERT: J 83 PHE cc_start: 0.4625 (m-80) cc_final: 0.3155 (p90) REVERT: J 119 LEU cc_start: 0.9188 (mt) cc_final: 0.8747 (mp) REVERT: J 136 LEU cc_start: 0.8108 (pt) cc_final: 0.7678 (tp) REVERT: K 1 MET cc_start: 0.7610 (tpp) cc_final: 0.7374 (tpp) REVERT: K 15 VAL cc_start: 0.9429 (t) cc_final: 0.9201 (p) REVERT: K 70 VAL cc_start: 0.8891 (m) cc_final: 0.8477 (p) REVERT: L 107 TYR cc_start: 0.8601 (m-80) cc_final: 0.8134 (m-10) REVERT: L 153 ASP cc_start: 0.8403 (m-30) cc_final: 0.7993 (t0) REVERT: L 169 PHE cc_start: 0.8688 (t80) cc_final: 0.8225 (t80) REVERT: L 187 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7262 (pm20) REVERT: L 223 MET cc_start: 0.8077 (ptt) cc_final: 0.7321 (ptp) REVERT: L 265 ASP cc_start: 0.6978 (p0) cc_final: 0.6637 (t0) REVERT: L 361 GLN cc_start: 0.7883 (tt0) cc_final: 0.6695 (mp10) REVERT: L 412 LEU cc_start: 0.8738 (mt) cc_final: 0.8538 (mt) REVERT: M 122 PHE cc_start: 0.8768 (t80) cc_final: 0.8312 (t80) REVERT: M 132 MET cc_start: 0.8983 (ptm) cc_final: 0.8525 (ptp) REVERT: M 135 LEU cc_start: 0.9365 (mt) cc_final: 0.8677 (tp) REVERT: M 148 PHE cc_start: 0.8998 (t80) cc_final: 0.8639 (t80) REVERT: M 204 LYS cc_start: 0.8436 (tppt) cc_final: 0.8080 (tppp) REVERT: M 434 LEU cc_start: 0.9072 (mm) cc_final: 0.8791 (pp) REVERT: M 443 MET cc_start: 0.8401 (tpp) cc_final: 0.8187 (tpp) REVERT: N 83 GLU cc_start: 0.8171 (mp0) cc_final: 0.7933 (mp0) REVERT: N 135 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8662 (mttp) REVERT: N 251 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8788 (mm-40) REVERT: N 265 HIS cc_start: 0.8009 (m-70) cc_final: 0.7430 (m-70) REVERT: N 269 MET cc_start: 0.7990 (mpp) cc_final: 0.7637 (mpp) REVERT: N 318 LYS cc_start: 0.7126 (mttt) cc_final: 0.6644 (mmtt) REVERT: N 345 LYS cc_start: 0.9179 (mttp) cc_final: 0.8706 (mttm) REVERT: N 375 TYR cc_start: 0.9103 (m-10) cc_final: 0.8734 (m-80) REVERT: N 420 LEU cc_start: 0.8611 (tp) cc_final: 0.8324 (tt) REVERT: H 79 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7166 (ttp-170) REVERT: H 124 TYR cc_start: 0.8309 (t80) cc_final: 0.7861 (t80) REVERT: H 170 LEU cc_start: 0.9165 (mm) cc_final: 0.8716 (tp) REVERT: H 186 VAL cc_start: 0.8954 (t) cc_final: 0.8463 (t) REVERT: H 189 GLN cc_start: 0.8639 (mp10) cc_final: 0.7897 (mp10) REVERT: H 314 PHE cc_start: 0.8693 (t80) cc_final: 0.7807 (t80) REVERT: H 328 VAL cc_start: 0.8710 (t) cc_final: 0.8451 (t) outliers start: 1 outliers final: 1 residues processed: 861 average time/residue: 0.2068 time to fit residues: 302.8866 Evaluate side-chains 666 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 665 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 117 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 419 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 366 optimal weight: 3.9990 chunk 278 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 343 ASN 2 81 GLN ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 24 ASN ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094437 restraints weight = 95552.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096528 restraints weight = 60248.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097953 restraints weight = 37461.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.098431 restraints weight = 28803.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098560 restraints weight = 24487.106| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.260 37092 Z= 0.398 Angle : 2.613 65.579 50559 Z= 1.474 Chirality : 0.444 6.478 5664 Planarity : 0.005 0.059 6374 Dihedral : 6.154 175.704 5088 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.92 % Favored : 94.80 % Rotamer: Outliers : 0.03 % Allowed : 1.26 % Favored : 98.71 % 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: 1.06 (0.10), residues: 2477 sheet: -1.35 (0.28), residues: 312 loop : -1.84 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 49 TYR 0.030 0.002 TYR L 416 PHE 0.038 0.002 PHE 4 160 TRP 0.071 0.002 TRP A 79 HIS 0.020 0.001 HIS 2 177 Details of bonding type rmsd/Z covalent geometry : bond 0.01159 / 0.40 (37052) covalent geometry : angle 2.25357 / 1.47 (50464) SS BOND : bond 0.01736 / 0.91 ( 1) SS BOND : angle 6.33508 / 2.88 ( 2) hydrogen bonds : bond 0.04307 / 2.91 ( 1889) hydrogen bonds : angle 4.71174 / 3.29 ( 5490) metal coordination : bond 0.02868 / 2.20 ( 37) metal coordination : angle 30.88538 / 21.30 ( 93) Misc. bond : bond 0.00347 / 0.17 ( 2) *********************** 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 876 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 875 time to evaluate : 1.270 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: 1 191 SER cc_start: 0.8926 (m) cc_final: 0.8531 (m) REVERT: 1 227 VAL cc_start: 0.8269 (t) cc_final: 0.7782 (p) REVERT: 1 238 PHE cc_start: 0.8005 (t80) cc_final: 0.7526 (t80) REVERT: 1 249 MET cc_start: 0.7016 (pmm) cc_final: 0.6618 (pmm) REVERT: 1 268 MET cc_start: 0.6703 (mtm) cc_final: 0.5527 (mpp) REVERT: 1 367 MET cc_start: 0.8701 (mtp) cc_final: 0.8252 (mtt) REVERT: 2 28 MET cc_start: 0.7952 (mtp) cc_final: 0.7576 (mtp) REVERT: 2 78 TYR cc_start: 0.8364 (m-80) cc_final: 0.7767 (m-10) REVERT: 2 89 LYS cc_start: 0.7590 (tptt) cc_final: 0.6671 (tppt) REVERT: 2 161 LYS cc_start: 0.8066 (mttm) cc_final: 0.7844 (mmmm) REVERT: 3 91 MET cc_start: 0.8468 (ttp) cc_final: 0.8263 (ttp) REVERT: 3 132 ASP cc_start: 0.9047 (m-30) cc_final: 0.8541 (m-30) REVERT: 3 200 LEU cc_start: 0.9061 (mm) cc_final: 0.8797 (mm) REVERT: 3 236 LEU cc_start: 0.8745 (mt) cc_final: 0.8533 (mt) REVERT: 3 249 MET cc_start: 0.8858 (mmt) cc_final: 0.8588 (mmm) REVERT: 3 395 PHE cc_start: 0.8741 (t80) cc_final: 0.8385 (t80) REVERT: 3 558 TRP cc_start: 0.6778 (p-90) cc_final: 0.6452 (p-90) REVERT: 3 595 GLU cc_start: 0.7693 (tp30) cc_final: 0.7428 (tp30) REVERT: 4 93 HIS cc_start: 0.8385 (m-70) cc_final: 0.7949 (m-70) REVERT: 4 130 LEU cc_start: 0.9379 (mm) cc_final: 0.9033 (mm) REVERT: 4 159 LEU cc_start: 0.8735 (tt) cc_final: 0.8526 (tt) REVERT: 4 197 LEU cc_start: 0.9295 (mt) cc_final: 0.9007 (tt) REVERT: 4 371 ARG cc_start: 0.8581 (tmt-80) cc_final: 0.8365 (tpt170) REVERT: 4 385 CYS cc_start: 0.7824 (p) cc_final: 0.7500 (t) REVERT: 4 393 MET cc_start: 0.7785 (tpt) cc_final: 0.7119 (tpt) REVERT: 5 3 LEU cc_start: 0.8111 (tt) cc_final: 0.7898 (mp) REVERT: 5 13 LYS cc_start: 0.7899 (mttt) cc_final: 0.7560 (mtmt) REVERT: 5 116 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7498 (mtp85) REVERT: 5 146 LEU cc_start: 0.9389 (mt) cc_final: 0.9012 (tt) REVERT: 5 185 LYS cc_start: 0.8643 (pttt) cc_final: 0.8279 (pttt) REVERT: 6 99 MET cc_start: 0.8357 (mtp) cc_final: 0.8097 (mtp) REVERT: 6 103 LYS cc_start: 0.8301 (pttt) cc_final: 0.8022 (ptpp) REVERT: 6 114 SER cc_start: 0.9037 (m) cc_final: 0.8603 (p) REVERT: 9 95 MET cc_start: 0.8533 (mmm) cc_final: 0.7981 (mmm) REVERT: 9 135 ASP cc_start: 0.7562 (m-30) cc_final: 0.7356 (t0) REVERT: 7 116 PHE cc_start: 0.8443 (m-10) cc_final: 0.8026 (m-80) REVERT: A 11 LEU cc_start: 0.8697 (mt) cc_final: 0.8064 (tt) REVERT: A 57 PHE cc_start: 0.8425 (m-80) cc_final: 0.8020 (m-80) REVERT: A 81 TYR cc_start: 0.8547 (t80) cc_final: 0.8172 (t80) REVERT: J 47 ASP cc_start: 0.8626 (t0) cc_final: 0.7479 (t0) REVERT: J 83 PHE cc_start: 0.4731 (m-80) cc_final: 0.3300 (p90) REVERT: J 119 LEU cc_start: 0.9147 (mt) cc_final: 0.8624 (mp) REVERT: J 136 LEU cc_start: 0.8195 (pt) cc_final: 0.7890 (tp) REVERT: K 15 VAL cc_start: 0.9421 (t) cc_final: 0.9197 (p) REVERT: K 70 VAL cc_start: 0.8897 (m) cc_final: 0.8495 (p) REVERT: L 78 LEU cc_start: 0.8131 (mt) cc_final: 0.7561 (pp) REVERT: L 107 TYR cc_start: 0.8606 (m-80) cc_final: 0.8102 (m-10) REVERT: L 110 LEU cc_start: 0.8809 (tp) cc_final: 0.8360 (tt) REVERT: L 129 ILE cc_start: 0.8931 (mt) cc_final: 0.8630 (mt) REVERT: L 153 ASP cc_start: 0.8353 (m-30) cc_final: 0.7858 (t0) REVERT: L 169 PHE cc_start: 0.8671 (t80) cc_final: 0.8372 (t80) REVERT: L 223 MET cc_start: 0.7960 (ptt) cc_final: 0.7179 (ptp) REVERT: L 265 ASP cc_start: 0.7087 (p0) cc_final: 0.6733 (t0) REVERT: L 361 GLN cc_start: 0.7584 (tt0) cc_final: 0.6393 (mp10) REVERT: L 373 LEU cc_start: 0.7700 (tp) cc_final: 0.7488 (tt) REVERT: L 449 LEU cc_start: 0.8279 (tp) cc_final: 0.8048 (tp) REVERT: L 471 PRO cc_start: 0.7667 (Cg_exo) cc_final: 0.7403 (Cg_endo) REVERT: M 122 PHE cc_start: 0.8783 (t80) cc_final: 0.8477 (t80) REVERT: M 132 MET cc_start: 0.9075 (ptm) cc_final: 0.8681 (ptp) REVERT: M 135 LEU cc_start: 0.9378 (mt) cc_final: 0.8678 (tp) REVERT: M 148 PHE cc_start: 0.8959 (t80) cc_final: 0.8611 (t80) REVERT: M 153 LEU cc_start: 0.9439 (mp) cc_final: 0.9150 (mt) REVERT: M 434 LEU cc_start: 0.9028 (mm) cc_final: 0.8741 (pp) REVERT: N 35 LEU cc_start: 0.9132 (tp) cc_final: 0.8888 (tp) REVERT: N 135 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8685 (mtmm) REVERT: N 265 HIS cc_start: 0.7595 (m-70) cc_final: 0.6878 (m-70) REVERT: N 269 MET cc_start: 0.8085 (mpp) cc_final: 0.7699 (mpp) REVERT: N 318 LYS cc_start: 0.6972 (mttt) cc_final: 0.6562 (mmtt) REVERT: N 345 LYS cc_start: 0.9243 (mttp) cc_final: 0.8806 (mttm) REVERT: N 375 TYR cc_start: 0.8968 (m-10) cc_final: 0.8591 (m-10) REVERT: N 420 LEU cc_start: 0.8565 (tp) cc_final: 0.8247 (tt) REVERT: H 79 ARG cc_start: 0.7920 (mmt180) cc_final: 0.6848 (ttp-170) REVERT: H 124 TYR cc_start: 0.8249 (t80) cc_final: 0.7736 (t80) REVERT: H 170 LEU cc_start: 0.9097 (mm) cc_final: 0.8764 (tp) REVERT: H 189 GLN cc_start: 0.8548 (mp10) cc_final: 0.8010 (mp10) REVERT: H 314 PHE cc_start: 0.8621 (t80) cc_final: 0.7721 (t80) REVERT: H 328 VAL cc_start: 0.8701 (t) cc_final: 0.8463 (t) outliers start: 1 outliers final: 0 residues processed: 875 average time/residue: 0.2031 time to fit residues: 303.0998 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 : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 307 optimal weight: 9.9990 chunk 262 optimal weight: 0.7980 chunk 417 optimal weight: 2.9990 chunk 442 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 346 optimal weight: 0.9980 chunk 394 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 81 GLN 2 135 GLN ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 379 GLN ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 582 GLN N 60 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094939 restraints weight = 96155.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096928 restraints weight = 58541.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098754 restraints weight = 37462.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099086 restraints weight = 27899.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099252 restraints weight = 23338.285| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.267 37092 Z= 0.397 Angle : 2.612 66.730 50559 Z= 1.473 Chirality : 0.445 6.612 5664 Planarity : 0.005 0.058 6374 Dihedral : 6.103 177.150 5088 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.05 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -0.28 (0.13), residues: 4612 helix: 1.10 (0.11), residues: 2471 sheet: -1.34 (0.28), residues: 314 loop : -1.81 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 49 TYR 0.031 0.001 TYR L 416 PHE 0.038 0.002 PHE 4 160 TRP 0.067 0.002 TRP A 79 HIS 0.011 0.001 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01158 / 0.40 (37052) covalent geometry : angle 2.25384 / 1.47 (50464) SS BOND : bond 0.00710 / 0.37 ( 1) SS BOND : angle 4.37749 / 1.99 ( 2) hydrogen bonds : bond 0.04218 / 2.87 ( 1889) hydrogen bonds : angle 4.67168 / 3.26 ( 5490) metal coordination : bond 0.03253 / 2.48 ( 37) metal coordination : angle 30.85375 / 21.23 ( 93) Misc. bond : bond 0.00450 / 0.22 ( 2) *********************** 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 877 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 877 time to evaluate : 1.343 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: 1 191 SER cc_start: 0.8921 (m) cc_final: 0.8421 (m) REVERT: 1 219 ASN cc_start: 0.8637 (m-40) cc_final: 0.8425 (m-40) REVERT: 1 238 PHE cc_start: 0.8235 (t80) cc_final: 0.7728 (t80) REVERT: 1 249 MET cc_start: 0.7308 (pmm) cc_final: 0.6968 (pmm) REVERT: 1 268 MET cc_start: 0.6691 (mtm) cc_final: 0.5529 (mpp) REVERT: 1 308 ASP cc_start: 0.8036 (p0) cc_final: 0.7703 (m-30) REVERT: 1 367 MET cc_start: 0.8789 (mtp) cc_final: 0.8376 (mtt) REVERT: 2 28 MET cc_start: 0.7826 (mtp) cc_final: 0.7395 (mtp) REVERT: 2 58 THR cc_start: 0.9156 (m) cc_final: 0.8765 (m) REVERT: 2 71 GLN cc_start: 0.7680 (mt0) cc_final: 0.7015 (mt0) REVERT: 2 78 TYR cc_start: 0.8455 (m-80) cc_final: 0.7674 (m-10) REVERT: 2 89 LYS cc_start: 0.7532 (tptt) cc_final: 0.6651 (tppt) REVERT: 3 132 ASP cc_start: 0.9090 (m-30) cc_final: 0.8567 (m-30) REVERT: 3 236 LEU cc_start: 0.8754 (mt) cc_final: 0.8506 (mt) REVERT: 3 249 MET cc_start: 0.8853 (mmt) cc_final: 0.8604 (mmm) REVERT: 3 395 PHE cc_start: 0.8754 (t80) cc_final: 0.8433 (t80) REVERT: 4 80 THR cc_start: 0.9580 (p) cc_final: 0.9345 (t) REVERT: 4 93 HIS cc_start: 0.8497 (m-70) cc_final: 0.7928 (m-70) REVERT: 4 130 LEU cc_start: 0.9445 (mm) cc_final: 0.8998 (mm) REVERT: 4 157 LEU cc_start: 0.9059 (mm) cc_final: 0.8854 (mp) REVERT: 4 197 LEU cc_start: 0.9267 (mt) cc_final: 0.8972 (tt) REVERT: 4 276 MET cc_start: 0.8576 (mmp) cc_final: 0.8345 (tpp) REVERT: 4 294 LEU cc_start: 0.9197 (tp) cc_final: 0.8995 (tt) REVERT: 4 371 ARG cc_start: 0.8574 (tmt-80) cc_final: 0.8350 (tpt170) REVERT: 4 385 CYS cc_start: 0.7762 (p) cc_final: 0.7502 (t) REVERT: 4 393 MET cc_start: 0.7737 (tpt) cc_final: 0.7097 (tpt) REVERT: 5 13 LYS cc_start: 0.7803 (mttt) cc_final: 0.7440 (mtmt) REVERT: 5 116 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7324 (mtp85) REVERT: 5 146 LEU cc_start: 0.9364 (mt) cc_final: 0.8952 (tt) REVERT: 5 185 LYS cc_start: 0.8589 (pttt) cc_final: 0.8122 (pttt) REVERT: 6 22 THR cc_start: 0.8102 (p) cc_final: 0.7682 (m) REVERT: 6 103 LYS cc_start: 0.8309 (pttt) cc_final: 0.8038 (ptpp) REVERT: 6 113 SER cc_start: 0.9338 (m) cc_final: 0.9030 (p) REVERT: 6 114 SER cc_start: 0.9002 (m) cc_final: 0.8619 (p) REVERT: 6 145 GLU cc_start: 0.8960 (mp0) cc_final: 0.8659 (mp0) REVERT: 6 177 LYS cc_start: 0.8197 (tmmt) cc_final: 0.6929 (tptp) REVERT: 9 69 TYR cc_start: 0.8941 (t80) cc_final: 0.8104 (t80) REVERT: 9 90 VAL cc_start: 0.9100 (t) cc_final: 0.8748 (t) REVERT: 9 95 MET cc_start: 0.8563 (mmm) cc_final: 0.7938 (mmm) REVERT: 9 135 ASP cc_start: 0.7645 (m-30) cc_final: 0.7353 (t0) REVERT: 7 116 PHE cc_start: 0.8455 (m-10) cc_final: 0.8060 (m-10) REVERT: A 11 LEU cc_start: 0.8827 (mt) cc_final: 0.8131 (tt) REVERT: A 57 PHE cc_start: 0.8335 (m-80) cc_final: 0.7915 (m-80) REVERT: A 81 TYR cc_start: 0.8542 (t80) cc_final: 0.8182 (t80) REVERT: J 47 ASP cc_start: 0.8608 (t0) cc_final: 0.7502 (t0) REVERT: J 83 PHE cc_start: 0.4720 (m-80) cc_final: 0.3310 (p90) REVERT: J 119 LEU cc_start: 0.9132 (mt) cc_final: 0.8635 (mp) REVERT: J 136 LEU cc_start: 0.7911 (pt) cc_final: 0.7686 (tp) REVERT: K 15 VAL cc_start: 0.9420 (t) cc_final: 0.9189 (p) REVERT: K 70 VAL cc_start: 0.8783 (m) cc_final: 0.8567 (p) REVERT: L 107 TYR cc_start: 0.8551 (m-80) cc_final: 0.8148 (m-10) REVERT: L 110 LEU cc_start: 0.8457 (tp) cc_final: 0.8013 (tt) REVERT: L 153 ASP cc_start: 0.8325 (m-30) cc_final: 0.7847 (t0) REVERT: L 169 PHE cc_start: 0.8693 (t80) cc_final: 0.8343 (t80) REVERT: L 223 MET cc_start: 0.7954 (ptt) cc_final: 0.7159 (ptp) REVERT: L 265 ASP cc_start: 0.7114 (p0) cc_final: 0.6745 (t0) REVERT: L 292 LYS cc_start: 0.6729 (mttt) cc_final: 0.6182 (mtpt) REVERT: L 319 LEU cc_start: 0.9145 (mt) cc_final: 0.8881 (mm) REVERT: L 361 GLN cc_start: 0.7496 (tt0) cc_final: 0.6164 (mp10) REVERT: L 449 LEU cc_start: 0.8288 (tp) cc_final: 0.8003 (tp) REVERT: L 471 PRO cc_start: 0.7775 (Cg_exo) cc_final: 0.7473 (Cg_endo) REVERT: M 102 MET cc_start: 0.8551 (tpp) cc_final: 0.8145 (tpp) REVERT: M 107 LEU cc_start: 0.9183 (mt) cc_final: 0.8977 (mt) REVERT: M 122 PHE cc_start: 0.8648 (t80) cc_final: 0.8246 (t80) REVERT: M 132 MET cc_start: 0.9090 (ptm) cc_final: 0.8687 (ptp) REVERT: M 135 LEU cc_start: 0.9321 (mt) cc_final: 0.8539 (tp) REVERT: M 148 PHE cc_start: 0.8937 (t80) cc_final: 0.8593 (t80) REVERT: M 434 LEU cc_start: 0.9058 (mm) cc_final: 0.8796 (pp) REVERT: N 35 LEU cc_start: 0.9100 (tp) cc_final: 0.8882 (tp) REVERT: N 62 PHE cc_start: 0.8346 (m-80) cc_final: 0.8103 (m-80) REVERT: N 83 GLU cc_start: 0.8275 (mp0) cc_final: 0.7995 (mp0) REVERT: N 125 ARG cc_start: 0.7376 (tpt90) cc_final: 0.7021 (mtm-85) REVERT: N 265 HIS cc_start: 0.7642 (m-70) cc_final: 0.6788 (m-70) REVERT: N 269 MET cc_start: 0.8092 (mpp) cc_final: 0.7685 (mpp) REVERT: N 318 LYS cc_start: 0.6986 (mttt) cc_final: 0.6592 (mmtt) REVERT: N 345 LYS cc_start: 0.9257 (mttp) cc_final: 0.8807 (mttm) REVERT: N 346 TYR cc_start: 0.8896 (t80) cc_final: 0.8601 (t80) REVERT: N 375 TYR cc_start: 0.9102 (m-10) cc_final: 0.8427 (m-10) REVERT: N 420 LEU cc_start: 0.8538 (tp) cc_final: 0.8188 (tt) REVERT: H 79 ARG cc_start: 0.7918 (mmt180) cc_final: 0.6845 (ttp-170) REVERT: H 124 TYR cc_start: 0.8261 (t80) cc_final: 0.7744 (t80) REVERT: H 125 LEU cc_start: 0.8464 (tp) cc_final: 0.8247 (tp) REVERT: H 170 LEU cc_start: 0.9223 (mm) cc_final: 0.8967 (tp) REVERT: H 181 ASN cc_start: 0.7764 (t0) cc_final: 0.7533 (t0) REVERT: H 189 GLN cc_start: 0.8592 (mp10) cc_final: 0.8058 (mp10) REVERT: H 314 PHE cc_start: 0.8534 (t80) cc_final: 0.7711 (t80) REVERT: H 328 VAL cc_start: 0.8705 (t) cc_final: 0.8457 (t) outliers start: 0 outliers final: 0 residues processed: 877 average time/residue: 0.2092 time to fit residues: 310.6982 Evaluate side-chains 691 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 691 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 279 optimal weight: 9.9990 chunk 115 optimal weight: 0.0010 chunk 409 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 342 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 452 optimal weight: 2.9990 chunk 364 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 81 GLN 2 135 GLN ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 582 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094679 restraints weight = 96070.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096260 restraints weight = 63190.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097806 restraints weight = 43836.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098191 restraints weight = 34937.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098263 restraints weight = 27914.266| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.264 37092 Z= 0.402 Angle : 2.621 67.509 50559 Z= 1.476 Chirality : 0.445 6.542 5664 Planarity : 0.005 0.058 6374 Dihedral : 6.112 178.809 5088 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.23 % Favored : 94.54 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % 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: -0.34 (0.12), residues: 4612 helix: 1.05 (0.10), residues: 2470 sheet: -1.38 (0.29), residues: 309 loop : -1.82 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 2 24 TYR 0.034 0.002 TYR L 416 PHE 0.040 0.002 PHE 4 160 TRP 0.086 0.002 TRP A 79 HIS 0.011 0.001 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.40 (37052) covalent geometry : angle 2.26141 / 1.47 (50464) SS BOND : bond 0.00528 / 0.28 ( 1) SS BOND : angle 4.36725 / 1.99 ( 2) hydrogen bonds : bond 0.04277 / 2.91 ( 1889) hydrogen bonds : angle 4.70168 / 3.28 ( 5490) metal coordination : bond 0.03497 / 2.64 ( 37) metal coordination : angle 30.99369 / 21.22 ( 93) Misc. bond : bond 0.00426 / 0.21 ( 2) ********************** 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 838 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 837 time to evaluate : 1.303 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 79 MET cc_start: 0.7934 (mmm) cc_final: 0.7731 (mtp) REVERT: 1 189 MET cc_start: 0.7184 (mtm) cc_final: 0.6915 (mtm) REVERT: 1 191 SER cc_start: 0.8937 (m) cc_final: 0.8443 (m) REVERT: 1 238 PHE cc_start: 0.7959 (t80) cc_final: 0.7529 (t80) REVERT: 1 249 MET cc_start: 0.7271 (pmm) cc_final: 0.6950 (pmm) REVERT: 1 268 MET cc_start: 0.6497 (mtm) cc_final: 0.5831 (mpp) REVERT: 1 308 ASP cc_start: 0.7983 (p0) cc_final: 0.7698 (m-30) REVERT: 1 367 MET cc_start: 0.8734 (mtp) cc_final: 0.8362 (mtt) REVERT: 2 28 MET cc_start: 0.7708 (mtp) cc_final: 0.7272 (mtp) REVERT: 2 89 LYS cc_start: 0.7492 (tptt) cc_final: 0.6647 (tptp) REVERT: 3 47 MET cc_start: 0.8947 (mmt) cc_final: 0.8709 (mmt) REVERT: 3 132 ASP cc_start: 0.9051 (m-30) cc_final: 0.8561 (m-30) REVERT: 3 236 LEU cc_start: 0.8709 (mt) cc_final: 0.8487 (mt) REVERT: 3 395 PHE cc_start: 0.8696 (t80) cc_final: 0.8357 (t80) REVERT: 3 413 LEU cc_start: 0.9335 (mt) cc_final: 0.9133 (mt) REVERT: 3 494 LYS cc_start: 0.8213 (tptp) cc_final: 0.7717 (tptp) REVERT: 4 80 THR cc_start: 0.9620 (p) cc_final: 0.9385 (t) REVERT: 4 93 HIS cc_start: 0.8420 (m-70) cc_final: 0.7925 (m-70) REVERT: 4 130 LEU cc_start: 0.9333 (mm) cc_final: 0.8934 (mm) REVERT: 4 159 LEU cc_start: 0.8974 (tt) cc_final: 0.8730 (tt) REVERT: 4 197 LEU cc_start: 0.9284 (mt) cc_final: 0.8976 (tt) REVERT: 4 208 PHE cc_start: 0.6482 (m-80) cc_final: 0.6272 (m-80) REVERT: 4 393 MET cc_start: 0.7763 (tpt) cc_final: 0.7202 (tpt) REVERT: 5 13 LYS cc_start: 0.7666 (mttt) cc_final: 0.7351 (mtmt) REVERT: 5 116 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7346 (mtp85) REVERT: 5 146 LEU cc_start: 0.9480 (mt) cc_final: 0.8933 (tt) REVERT: 5 185 LYS cc_start: 0.8356 (pttt) cc_final: 0.8096 (pttt) REVERT: 6 22 THR cc_start: 0.7851 (p) cc_final: 0.7493 (m) REVERT: 6 69 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7240 (mtt180) REVERT: 6 114 SER cc_start: 0.8967 (m) cc_final: 0.8463 (p) REVERT: 6 177 LYS cc_start: 0.8310 (tmmt) cc_final: 0.7047 (tptp) REVERT: 9 69 TYR cc_start: 0.8932 (t80) cc_final: 0.8105 (t80) REVERT: 9 90 VAL cc_start: 0.9147 (t) cc_final: 0.8809 (t) REVERT: 9 95 MET cc_start: 0.8616 (mmm) cc_final: 0.8006 (mmm) REVERT: 9 135 ASP cc_start: 0.7839 (m-30) cc_final: 0.7498 (t0) REVERT: 7 105 THR cc_start: 0.7934 (m) cc_final: 0.7348 (p) REVERT: 7 116 PHE cc_start: 0.8432 (m-10) cc_final: 0.8085 (m-10) REVERT: A 11 LEU cc_start: 0.8692 (mt) cc_final: 0.8054 (tt) REVERT: A 57 PHE cc_start: 0.8259 (m-80) cc_final: 0.7838 (m-80) REVERT: A 81 TYR cc_start: 0.8444 (t80) cc_final: 0.8082 (t80) REVERT: J 20 VAL cc_start: 0.9375 (m) cc_final: 0.9144 (p) REVERT: J 47 ASP cc_start: 0.8663 (t0) cc_final: 0.7571 (t0) REVERT: J 83 PHE cc_start: 0.4742 (m-80) cc_final: 0.3357 (p90) REVERT: J 119 LEU cc_start: 0.9033 (mt) cc_final: 0.8534 (mp) REVERT: K 7 SER cc_start: 0.9480 (m) cc_final: 0.9228 (p) REVERT: K 15 VAL cc_start: 0.9397 (t) cc_final: 0.9183 (p) REVERT: K 70 VAL cc_start: 0.9007 (m) cc_final: 0.8637 (p) REVERT: L 107 TYR cc_start: 0.8431 (m-10) cc_final: 0.8112 (m-10) REVERT: L 110 LEU cc_start: 0.8489 (tp) cc_final: 0.8119 (tt) REVERT: L 128 PHE cc_start: 0.8814 (t80) cc_final: 0.8301 (t80) REVERT: L 134 VAL cc_start: 0.9201 (t) cc_final: 0.8957 (t) REVERT: L 153 ASP cc_start: 0.8266 (m-30) cc_final: 0.7779 (t0) REVERT: L 169 PHE cc_start: 0.8657 (t80) cc_final: 0.8193 (t80) REVERT: L 173 MET cc_start: 0.8910 (mmm) cc_final: 0.8591 (mmm) REVERT: L 265 ASP cc_start: 0.7058 (p0) cc_final: 0.6720 (t0) REVERT: L 292 LYS cc_start: 0.6811 (mttt) cc_final: 0.6172 (mtpt) REVERT: L 319 LEU cc_start: 0.9121 (mt) cc_final: 0.8915 (mm) REVERT: L 361 GLN cc_start: 0.7227 (tt0) cc_final: 0.5779 (mp10) REVERT: M 132 MET cc_start: 0.9010 (ptm) cc_final: 0.8559 (ptp) REVERT: M 148 PHE cc_start: 0.8949 (t80) cc_final: 0.8586 (t80) REVERT: N 35 LEU cc_start: 0.9084 (tp) cc_final: 0.8869 (tp) REVERT: N 83 GLU cc_start: 0.8177 (mp0) cc_final: 0.7918 (mp0) REVERT: N 125 ARG cc_start: 0.7253 (tpt90) cc_final: 0.7025 (mtm-85) REVERT: N 265 HIS cc_start: 0.7949 (m-70) cc_final: 0.6987 (m-70) REVERT: N 269 MET cc_start: 0.7778 (mpp) cc_final: 0.7428 (mpp) REVERT: N 318 LYS cc_start: 0.7182 (mttt) cc_final: 0.6681 (mmtt) REVERT: N 345 LYS cc_start: 0.9239 (mttp) cc_final: 0.8809 (mttm) REVERT: N 346 TYR cc_start: 0.8828 (t80) cc_final: 0.8540 (t80) REVERT: N 375 TYR cc_start: 0.9089 (m-10) cc_final: 0.8442 (m-10) REVERT: N 420 LEU cc_start: 0.8503 (tp) cc_final: 0.8186 (tt) REVERT: H 79 ARG cc_start: 0.7902 (mmt180) cc_final: 0.6905 (ttp-170) REVERT: H 124 TYR cc_start: 0.8188 (t80) cc_final: 0.7678 (t80) REVERT: H 130 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8076 (tp30) REVERT: H 170 LEU cc_start: 0.9212 (mm) cc_final: 0.8899 (tp) REVERT: H 189 GLN cc_start: 0.8566 (mp10) cc_final: 0.8036 (mp10) REVERT: H 235 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7198 (mp0) REVERT: H 246 MET cc_start: 0.8655 (ttp) cc_final: 0.8400 (ttp) REVERT: H 314 PHE cc_start: 0.8501 (t80) cc_final: 0.7729 (t80) REVERT: H 328 VAL cc_start: 0.8732 (t) cc_final: 0.8498 (t) outliers start: 1 outliers final: 0 residues processed: 837 average time/residue: 0.1987 time to fit residues: 282.5445 Evaluate side-chains 677 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 677 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 454 optimal weight: 5.9990 chunk 326 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 430 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 chunk 113 optimal weight: 0.0070 chunk 444 optimal weight: 2.9990 chunk 317 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 81 GLN 2 135 GLN ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093897 restraints weight = 95348.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.095581 restraints weight = 66232.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096776 restraints weight = 43434.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097094 restraints weight = 35713.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097358 restraints weight = 29813.500| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.263 37092 Z= 0.404 Angle : 2.626 68.115 50559 Z= 1.478 Chirality : 0.445 6.533 5664 Planarity : 0.005 0.059 6374 Dihedral : 6.161 179.991 5088 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.42 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -0.40 (0.12), residues: 4612 helix: 0.97 (0.10), residues: 2482 sheet: -1.38 (0.29), residues: 307 loop : -1.82 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 2 24 TYR 0.031 0.002 TYR L 416 PHE 0.055 0.002 PHE H 290 TRP 0.077 0.002 TRP A 79 HIS 0.011 0.001 HIS M 211 Details of bonding type rmsd/Z covalent geometry : bond 0.01166 / 0.40 (37052) covalent geometry : angle 2.26512 / 1.47 (50464) SS BOND : bond 0.01175 / 0.62 ( 1) SS BOND : angle 3.75105 / 1.71 ( 2) hydrogen bonds : bond 0.04367 / 2.95 ( 1889) hydrogen bonds : angle 4.74081 / 3.30 ( 5490) metal coordination : bond 0.03386 / 2.56 ( 37) metal coordination : angle 31.04237 / 21.21 ( 93) Misc. bond : bond 0.00383 / 0.19 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7018.62 seconds wall clock time: 121 minutes 44.90 seconds (7304.90 seconds total)