Starting phenix.real_space_refine (version: dev) on Tue May 17 03:04:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/05_2022/6zjl_11235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/05_2022/6zjl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/05_2022/6zjl_11235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/05_2022/6zjl_11235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/05_2022/6zjl_11235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zjl_11235/05_2022/6zjl_11235_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "3 TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/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: {'PTRANS': 10, 'TRANS': 166, 'PCIS': 1} 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: {'PTRANS': 29, 'TRANS': 353, 'PCIS': 1} 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: {'PTRANS': 11, 'TRANS': 153, 'PCIS': 1} Chain: "9" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 15, 'TRANS': 163, 'PCIS': 1} 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: {'PTRANS': 28, 'TRANS': 575, 'PCIS': 1} Chain: "M" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3489 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 21, 'TRANS': 443, 'PCIS': 2} 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: {'PTRANS': 23, 'TRANS': 401, 'PCIS': 2} Chain: "H" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2838 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 17, 'TRANS': 333, 'PCIS': 2} 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: {'SF4': 3, 'FES': 1} 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: 19.69, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.94 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Iron sulfur cluster 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... running ksdssp... Secondary structure from input PDB file: 186 helices and 22 sheets defined 52.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain '1' and resid 29 through 35 Processing helix chain '1' and resid 39 through 47 Processing helix chain '1' and resid 50 through 60 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) Processing helix chain '1' and resid 72 through 77 Processing helix chain '1' and resid 102 through 109 removed outlier: 4.178A pdb=" N ILE 1 106 " --> pdb=" O LYS 1 102 " (cutoff:3.500A) Processing helix chain '1' and resid 111 through 124 Processing helix chain '1' and resid 140 through 155 Processing helix chain '1' and resid 180 through 183 Processing helix chain '1' and resid 185 through 193 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 211 through 213 No H-bonds generated for 'chain '1' and resid 211 through 213' Processing helix chain '1' and resid 221 through 233 removed outlier: 4.191A pdb=" N VAL 1 228 " --> pdb=" O LEU 1 224 " (cutoff:3.500A) Proline residue: 1 229 - end of helix Processing helix chain '1' and resid 235 through 239 Processing helix chain '1' and resid 272 through 277 Processing helix chain '1' and resid 304 through 307 No H-bonds generated for 'chain '1' and resid 304 through 307' Processing helix chain '1' and resid 317 through 319 No H-bonds generated for 'chain '1' and resid 317 through 319' Processing helix chain '1' and resid 337 through 350 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 357 through 365 removed outlier: 3.778A pdb=" N VAL 1 363 " --> pdb=" O CYS 1 359 " (cutoff:3.500A) Processing helix chain '1' and resid 367 through 376 Processing helix chain '1' and resid 381 through 397 Proline residue: 1 392 - end of helix removed outlier: 4.290A pdb=" N GLY 1 396 " --> pdb=" O PRO 1 392 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG 1 397 " --> pdb=" O LEU 1 393 " (cutoff:3.500A) Processing helix chain '1' and resid 402 through 416 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 418 through 426 Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 23 through 38 Proline residue: 2 29 - end of helix removed outlier: 3.648A pdb=" N GLN 2 36 " --> pdb=" O ARG 2 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU 2 37 " --> pdb=" O VAL 2 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU 2 38 " --> pdb=" O GLN 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 53 Processing helix chain '2' and resid 57 through 66 removed outlier: 3.605A pdb=" N PHE 2 66 " --> pdb=" O GLY 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 90 Processing helix chain '2' and resid 93 through 104 Processing helix chain '2' and resid 128 through 130 No H-bonds generated for 'chain '2' and resid 128 through 130' Processing helix chain '2' and resid 147 through 158 Processing helix chain '3' and resid 19 through 26 Processing helix chain '3' and resid 98 through 114 removed outlier: 5.006A pdb=" N ASN 3 114 " --> pdb=" O PHE 3 110 " (cutoff:3.500A) Processing helix chain '3' and resid 129 through 137 Processing helix chain '3' and resid 186 through 193 Processing helix chain '3' and resid 206 through 208 No H-bonds generated for 'chain '3' and resid 206 through 208' Processing helix chain '3' and resid 223 through 229 removed outlier: 3.863A pdb=" N ILE 3 226 " --> pdb=" O SER 3 223 " (cutoff:3.500A) Processing helix chain '3' and resid 238 through 240 No H-bonds generated for 'chain '3' and resid 238 through 240' Processing helix chain '3' and resid 246 through 248 No H-bonds generated for 'chain '3' and resid 246 through 248' Processing helix chain '3' and resid 292 through 295 No H-bonds generated for 'chain '3' and resid 292 through 295' Processing helix chain '3' and resid 322 through 333 removed outlier: 4.153A pdb=" N LEU 3 333 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) Processing helix chain '3' and resid 351 through 363 Processing helix chain '3' and resid 402 through 405 No H-bonds generated for 'chain '3' and resid 402 through 405' Processing helix chain '3' and resid 407 through 417 removed outlier: 3.636A pdb=" N VAL 3 417 " --> pdb=" O SER 3 414 " (cutoff:3.500A) Processing helix chain '3' and resid 458 through 461 Processing helix chain '3' and resid 473 through 481 Processing helix chain '3' and resid 488 through 499 Processing helix chain '3' and resid 515 through 527 removed outlier: 4.154A pdb=" N GLU 3 526 " --> pdb=" O ARG 3 522 " (cutoff:3.500A) Processing helix chain '3' and resid 541 through 546 Processing helix chain '3' and resid 574 through 577 No H-bonds generated for 'chain '3' and resid 574 through 577' Processing helix chain '3' and resid 607 through 609 No H-bonds generated for 'chain '3' and resid 607 through 609' Processing helix chain '3' and resid 637 through 648 Processing helix chain '3' and resid 657 through 667 removed outlier: 3.577A pdb=" N GLN 3 661 " --> pdb=" O HIS 3 657 " (cutoff:3.500A) Processing helix chain '3' and resid 701 through 703 No H-bonds generated for 'chain '3' and resid 701 through 703' Processing helix chain '3' and resid 708 through 711 No H-bonds generated for 'chain '3' and resid 708 through 711' Processing helix chain '3' and resid 720 through 725 Processing helix chain '4' and resid 66 through 72 removed outlier: 4.486A pdb=" N GLU 4 71 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N HIS 4 72 " --> pdb=" O LYS 4 68 " (cutoff:3.500A) Processing helix chain '4' and resid 75 through 80 removed outlier: 3.721A pdb=" N ILE 4 79 " --> pdb=" O TYR 4 75 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR 4 80 " --> pdb=" O LEU 4 76 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 75 through 80' Processing helix chain '4' and resid 82 through 84 No H-bonds generated for 'chain '4' and resid 82 through 84' Processing helix chain '4' and resid 90 through 105 removed outlier: 3.654A pdb=" N ASP 4 94 " --> pdb=" O SER 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 139 Processing helix chain '4' and resid 143 through 164 removed outlier: 3.575A pdb=" N TYR 4 148 " --> pdb=" O PRO 4 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU 4 152 " --> pdb=" O ALA 4 149 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR 4 164 " --> pdb=" O GLU 4 161 " (cutoff:3.500A) Processing helix chain '4' and resid 184 through 208 removed outlier: 3.676A pdb=" N VAL 4 187 " --> pdb=" O GLU 4 184 " (cutoff:3.500A) Proline residue: 4 188 - end of helix removed outlier: 3.587A pdb=" N VAL 4 196 " --> pdb=" O LEU 4 193 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU 4 197 " --> pdb=" O LEU 4 194 " (cutoff:3.500A) Proline residue: 4 198 - end of helix removed outlier: 3.643A pdb=" N ILE 4 201 " --> pdb=" O PRO 4 198 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP 4 202 " --> pdb=" O HIS 4 199 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA 4 206 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 218 removed outlier: 3.822A pdb=" N GLU 4 216 " --> pdb=" O PRO 4 212 " (cutoff:3.500A) Processing helix chain '4' and resid 226 through 231 Processing helix chain '4' and resid 240 through 242 No H-bonds generated for 'chain '4' and resid 240 through 242' Processing helix chain '4' and resid 248 through 251 No H-bonds generated for 'chain '4' and resid 248 through 251' Processing helix chain '4' and resid 257 through 259 No H-bonds generated for 'chain '4' and resid 257 through 259' Processing helix chain '4' and resid 272 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 321 through 332 Processing helix chain '4' and resid 373 through 377 Processing helix chain '4' and resid 379 through 384 removed outlier: 4.477A pdb=" N TYR 4 383 " --> pdb=" O GLN 4 379 " (cutoff:3.500A) Processing helix chain '4' and resid 390 through 400 removed outlier: 4.145A pdb=" N VAL 4 394 " --> pdb=" O VAL 4 390 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA 4 395 " --> pdb=" O PRO 4 391 " (cutoff:3.500A) 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 404 through 408 Processing helix chain '5' and resid 2 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 34 through 44 Processing helix chain '5' and resid 111 through 121 Processing helix chain '5' and resid 167 through 169 No H-bonds generated for 'chain '5' and resid 167 through 169' Processing helix chain '5' and resid 187 through 190 Processing helix chain '6' and resid 22 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 45 through 52 removed outlier: 3.731A pdb=" N GLU 6 49 " --> pdb=" O CYS 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 98 Proline residue: 6 90 - end of helix removed outlier: 3.774A pdb=" N ARG 6 93 " --> pdb=" O PRO 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 110 through 113 No H-bonds generated for 'chain '6' and resid 110 through 113' Processing helix chain '6' and resid 127 through 129 No H-bonds generated for 'chain '6' and resid 127 through 129' Processing helix chain '6' and resid 144 through 158 Processing helix chain '9' and resid 3 through 18 removed outlier: 3.573A pdb=" N LEU 9 6 " --> pdb=" O LEU 9 3 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER 9 9 " --> pdb=" O LEU 9 6 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 9 14 " --> pdb=" O GLY 9 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE 9 18 " --> pdb=" O LYS 9 15 " (cutoff:3.500A) Processing helix chain '9' and resid 58 through 62 Processing helix chain '9' and resid 103 through 107 Processing helix chain '9' and resid 126 through 129 Processing helix chain '9' and resid 133 through 135 No H-bonds generated for 'chain '9' and resid 133 through 135' Processing helix chain '9' and resid 144 through 152 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 27 removed outlier: 3.635A pdb=" N TYR 7 10 " --> pdb=" O ARG 7 7 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR 7 23 " --> pdb=" O MET 7 20 " (cutoff:3.500A) Processing helix chain '7' and resid 38 through 41 No H-bonds generated for 'chain '7' and resid 38 through 41' Processing helix chain '7' and resid 112 through 126 Processing helix chain 'A' and resid 5 through 30 removed outlier: 3.605A pdb=" N GLY A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 83 removed outlier: 3.763A pdb=" N VAL A 64 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 67 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 71 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Proline residue: A 80 - end of helix removed outlier: 3.821A pdb=" N VAL A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'J' and resid 2 through 21 removed outlier: 4.038A pdb=" N LEU J 7 " --> pdb=" O LEU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 88 through 109 Proline residue: J 91 - end of helix removed outlier: 3.617A pdb=" N ALA J 97 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL J 100 " --> pdb=" O ALA J 97 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 122 No H-bonds generated for 'chain 'J' and resid 120 through 122' Processing helix chain 'J' and resid 124 through 131 Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 136 through 157 Processing helix chain 'K' and resid 2 through 20 removed outlier: 3.760A pdb=" N ALA K 8 " --> pdb=" O LEU K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 49 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 52 through 79 Processing helix chain 'K' and resid 87 through 89 No H-bonds generated for 'chain 'K' and resid 87 through 89' Processing helix chain 'L' and resid 2 through 19 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 28 through 49 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 71 through 94 Processing helix chain 'L' and resid 101 through 119 Processing helix chain 'L' and resid 124 through 142 Processing helix chain 'L' and resid 150 through 178 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) Processing helix chain 'L' and resid 185 through 192 Processing helix chain 'L' and resid 199 through 216 removed outlier: 3.514A pdb=" N GLY L 215 " --> pdb=" O LEU L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 230 Processing helix chain 'L' and resid 234 through 241 Processing helix chain 'L' and resid 246 through 262 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) removed outlier: 5.500A pdb=" N PHE L 258 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU L 259 " --> pdb=" O ARG L 255 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL L 262 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 284 Processing helix chain 'L' and resid 291 through 312 removed outlier: 3.871A pdb=" N SER L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL L 312 " --> pdb=" O LEU L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 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 362 through 374 Processing helix chain 'L' and resid 380 through 394 removed outlier: 3.959A pdb=" N LEU L 393 " --> pdb=" O LEU L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 425 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 440 through 455 Proline residue: L 445 - end of helix Processing helix chain 'L' and resid 470 through 474 Processing helix chain 'L' and resid 491 through 511 removed outlier: 3.919A pdb=" N GLY L 508 " --> pdb=" O GLY L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 529 removed outlier: 3.713A pdb=" N ALA L 523 " --> pdb=" O ALA L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 541 removed outlier: 6.123A pdb=" N ASP L 535 " --> pdb=" O PHE L 532 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG L 536 " --> pdb=" O TYR L 533 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU L 541 " --> pdb=" O TYR L 538 " (cutoff:3.500A) Processing helix chain 'L' and resid 543 through 579 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 586 through 604 Processing helix chain 'M' and resid 2 through 17 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 23 through 41 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 59 No H-bonds generated for 'chain 'M' and resid 57 through 59' Processing helix chain 'M' and resid 71 through 88 removed outlier: 3.617A pdb=" N LEU M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 111 Processing helix chain 'M' and resid 115 through 134 removed outlier: 4.248A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 141 through 168 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 177 through 182 Processing helix chain 'M' and resid 190 through 202 removed outlier: 4.042A pdb=" N ALA M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 210 No H-bonds generated for 'chain 'M' and resid 208 through 210' Processing helix chain 'M' and resid 212 through 220 Proline residue: M 216 - end of helix Processing helix chain 'M' and resid 226 through 232 Processing helix chain 'M' and resid 237 through 243 Processing helix chain 'M' and resid 245 through 248 No H-bonds generated for 'chain 'M' and resid 245 through 248' Processing helix chain 'M' and resid 250 through 277 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) removed outlier: 4.708A pdb=" N ALA M 277 " --> pdb=" O TRP M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 302 Processing helix chain 'M' and resid 305 through 336 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 354 through 366 Processing helix chain 'M' and resid 372 through 387 removed outlier: 4.450A pdb=" N GLY M 376 " --> pdb=" O SER M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 414 removed outlier: 3.563A pdb=" N LEU M 397 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER M 398 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL M 399 " --> pdb=" O ALA M 395 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE M 400 " --> pdb=" O PHE M 396 " (cutoff:3.500A) 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 427 through 445 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 449 No H-bonds generated for 'chain 'M' and resid 447 through 449' Processing helix chain 'M' and resid 452 through 465 Proline residue: M 456 - end of helix removed outlier: 5.208A pdb=" N LEU M 465 " --> pdb=" O PHE M 461 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 18 removed outlier: 3.951A pdb=" N LEU N 15 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE N 18 " --> pdb=" O THR N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 43 Processing helix chain 'N' and resid 57 through 76 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) Processing helix chain 'N' and resid 82 through 99 removed outlier: 5.572A pdb=" N LEU N 87 " --> pdb=" O PHE N 84 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR N 90 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU N 97 " --> pdb=" O GLY N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 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 128 through 157 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 170 through 187 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 193 through 202 Proline residue: N 197 - end of helix removed outlier: 3.873A pdb=" N TYR N 200 " --> pdb=" O PRO N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 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 230 through 250 removed outlier: 3.626A pdb=" N ALA N 234 " --> pdb=" O PRO N 230 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU N 249 " --> pdb=" O ASN N 245 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA N 250 " --> pdb=" O LEU N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 272 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) Processing helix chain 'N' and resid 280 through 302 Processing helix chain 'N' and resid 309 through 312 Processing helix chain 'N' and resid 315 through 318 No H-bonds generated for 'chain 'N' and resid 315 through 318' Processing helix chain 'N' and resid 320 through 334 Processing helix chain 'N' and resid 340 through 355 removed outlier: 3.574A pdb=" N ALA N 348 " --> pdb=" O GLY N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 379 removed outlier: 3.523A pdb=" N VAL N 370 " --> pdb=" O VAL N 366 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR N 373 " --> pdb=" O ALA N 369 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR N 374 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 381 through 383 No H-bonds generated for 'chain 'N' and resid 381 through 383' Processing helix chain 'N' and resid 396 through 414 Processing helix chain 'N' and resid 416 through 422 Proline residue: N 421 - end of helix Processing helix chain 'H' and resid 10 through 42 removed outlier: 3.515A pdb=" N PHE H 42 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 79 through 94 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 121 through 143 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) Processing helix chain 'H' and resid 146 through 177 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 182 through 191 removed outlier: 3.515A pdb=" N GLU H 191 " --> pdb=" O ASN H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 211 Processing helix chain 'H' and resid 239 through 263 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 277 through 296 Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 313 through 329 Processing helix chain 'H' and resid 335 through 350 removed outlier: 4.000A pdb=" N LEU H 340 " --> pdb=" O TYR H 336 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 215 through 220 removed outlier: 3.657A pdb=" N TYR 1 88 " --> pdb=" O PRO 1 215 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL 1 129 " --> pdb=" O LEU 1 89 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N CYS 1 91 " --> pdb=" O VAL 1 129 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR 1 131 " --> pdb=" O CYS 1 91 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA 1 93 " --> pdb=" O TYR 1 131 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR 1 133 " --> pdb=" O ALA 1 93 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP 1 170 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE 1 132 " --> pdb=" O ASP 1 170 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS 1 172 " --> pdb=" O ILE 1 132 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL 1 134 " --> pdb=" O HIS 1 172 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS 1 174 " --> pdb=" O VAL 1 134 " (cutoff:3.500A) Processing sheet with id= B, 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= C, first strand: chain '1' and resid 287 through 291 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= D, first strand: chain '2' and resid 117 through 122 removed outlier: 5.967A pdb=" N TYR 2 78 " --> pdb=" O SER 2 118 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN 2 120 " --> pdb=" O TYR 2 78 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU 2 80 " --> pdb=" O GLN 2 120 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL 2 122 " --> pdb=" O LEU 2 80 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL 2 82 " --> pdb=" O VAL 2 122 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 9 through 11 removed outlier: 5.722A pdb=" N MET 3 91 " --> pdb=" O LYS 3 5 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 235 through 237 removed outlier: 3.711A pdb=" N SER 3 171 " --> pdb=" O VAL 3 174 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU 3 176 " --> pdb=" O PRO 3 169 " (cutoff:3.500A) Processing sheet with id= G, 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= H, first strand: chain '3' and resid 310 through 312 Processing sheet with id= I, first strand: chain '3' and resid 369 through 371 removed outlier: 8.146A pdb=" N ASP 3 370 " --> pdb=" O VAL 3 341 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU 3 343 " --> pdb=" O ASP 3 370 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR 3 565 " --> pdb=" O GLY 3 342 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR 3 344 " --> pdb=" O TYR 3 565 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR 3 567 " --> pdb=" O TYR 3 344 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE 3 582 " --> pdb=" O ALA 3 566 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N TYR 3 568 " --> pdb=" O PHE 3 582 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL 3 584 " --> pdb=" O TYR 3 568 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL 3 600 " --> pdb=" O MET 3 585 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU 3 587 " --> pdb=" O VAL 3 600 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU 3 602 " --> pdb=" O LEU 3 587 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, 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: 6.478A pdb=" N LYS 3 531 " --> pdb=" O LEU 3 505 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU 3 507 " --> pdb=" O LYS 3 531 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU 3 533 " --> pdb=" O LEU 3 507 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 612 through 615 Processing sheet with id= L, first strand: chain '3' and resid 692 through 696 removed outlier: 5.483A pdb=" N LEU 3 758 " --> pdb=" O TYR 3 693 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ARG 3 695 " --> pdb=" O LEU 3 758 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU 3 760 " --> pdb=" O ARG 3 695 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain '3' and resid 714 through 718 removed outlier: 4.271A pdb=" N ALA 3 714 " --> pdb=" O GLU 3 744 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 27 through 30 Processing sheet with id= O, first strand: chain '4' and resid 339 through 348 removed outlier: 4.173A pdb=" N VAL 4 344 " --> pdb=" O TYR 4 355 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR 4 355 " --> pdb=" O VAL 4 344 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 52 through 56 removed outlier: 3.554A pdb=" N PHE 5 68 " --> pdb=" O VAL 5 94 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 38 through 42 removed outlier: 5.613A pdb=" N VAL 6 77 " --> pdb=" O ALA 6 39 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE 6 41 " --> pdb=" O VAL 6 77 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE 6 79 " --> pdb=" O PHE 6 41 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP 6 104 " --> pdb=" O MET 6 78 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL 6 80 " --> pdb=" O TRP 6 104 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE 6 106 " --> pdb=" O VAL 6 80 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL 6 135 " --> pdb=" O SER 6 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '9' and resid 31 through 33 Processing sheet with id= S, first strand: chain '9' and resid 130 through 132 removed outlier: 3.548A pdb=" N LYS 9 89 " --> pdb=" O GLU 9 71 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU 9 71 " --> pdb=" O LYS 9 89 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR 9 91 " --> pdb=" O TYR 9 69 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR 9 69 " --> pdb=" O TYR 9 91 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '7' and resid 102 through 105 removed outlier: 4.168A pdb=" N ILE 7 91 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU 7 59 " --> pdb=" O PHE 7 67 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU 7 69 " --> pdb=" O ALA 7 57 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA 7 57 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR 7 56 " --> pdb=" O ALA 7 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER 7 58 " --> pdb=" O LYS 7 33 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS 7 33 " --> pdb=" O SER 7 58 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER 7 60 " --> pdb=" O PHE 7 31 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE 7 31 " --> pdb=" O SER 7 60 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 53 through 58 Processing sheet with id= V, first strand: chain 'M' and resid 51 through 56 removed outlier: 7.119A pdb=" N VAL M 61 " --> pdb=" O LEU M 55 " (cutoff:3.500A) 1597 hydrogen bonds defined for protein. 4353 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: 11.74 Time building geometry restraints manager: 16.08 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: 60.45 - 75.13: 87 75.13 - 89.80: 1 89.80 - 104.48: 1289 104.48 - 119.16: 29326 119.16 - 133.84: 19761 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 " 0.172 2.00e-02 2.50e+03 pdb=" CD2 TYR N 316 " 0.181 2.00e-02 2.50e+03 pdb=" CE1 TYR N 316 " 0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR N 316 " 0.105 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: 37279 3.26 - 3.80: 57836 3.80 - 4.35: 74207 4.35 - 4.90: 121655 Nonbonded interactions: 292926 Sorted by model distance: nonbonded pdb=" O2P FMN 1 502 " pdb=" O4' FMN 1 502 " model vdw 2.162 2.440 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 292921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 7.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 32.010 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.320 Process input model: 97.790 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.460 ------------------------------------------------------------------------------- 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 : 0.021 0.146 37052 Z= 1.383 Angle : 2.330 13.686 50464 Z= 1.560 Chirality : 1.407 20.964 5664 Planarity : 0.023 0.204 6374 Dihedral : 15.364 159.694 13228 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 2.86 % Allowed : 9.56 % Favored : 87.58 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 1430 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1341 time to evaluate : 4.207 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 outliers start: 89 outliers final: 26 residues processed: 1397 average time/residue: 0.4919 time to fit residues: 1119.7864 Evaluate side-chains 804 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 778 time to evaluate : 4.188 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4474 time to fit residues: 25.1718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 2.9990 chunk 346 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 233 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 chunk 358 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 415 optimal weight: 6.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 174 HIS 1 245 GLN 1 315 HIS 1 343 ASN 2 8 GLN 2 120 GLN 2 135 GLN ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 208 HIS 3 225 ASN 3 372 GLN 3 468 HIS 4 33 GLN 4 58 HIS 4 78 ASN ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 169 HIS 6 58 ASN J 24 ASN L 150 GLN L 325 HIS ** 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 411 GLN N 245 ASN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS H 245 GLN ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.277 37052 Z= 0.820 Angle : 2.292 51.186 50464 Z= 1.488 Chirality : 0.444 6.497 5664 Planarity : 0.008 0.104 6374 Dihedral : 7.279 163.149 5088 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.79 % Favored : 93.80 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.11), residues: 4612 helix: -0.68 (0.09), residues: 2464 sheet: -1.40 (0.30), residues: 270 loop : -2.62 (0.13), residues: 1878 *********************** 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 1120 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1113 time to evaluate : 4.197 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 outliers start: 7 outliers final: 2 residues processed: 1116 average time/residue: 0.4565 time to fit residues: 844.0462 Evaluate side-chains 754 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 752 time to evaluate : 3.986 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3018 time to fit residues: 6.4651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 230 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 345 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 415 optimal weight: 9.9990 chunk 449 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 412 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 333 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 208 GLN 2 129 HIS 2 137 ASN ** 2 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 38 HIS ** 3 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 183 HIS 3 392 GLN ** 3 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 468 HIS ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 HIS 4 72 HIS 4 129 HIS 5 24 ASN 6 120 ASN 6 153 GLN K 39 ASN ** L 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 513 GLN L 582 GLN N 60 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 HIS ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.281 37052 Z= 0.785 Angle : 2.286 50.909 50464 Z= 1.485 Chirality : 0.444 6.454 5664 Planarity : 0.006 0.106 6374 Dihedral : 6.787 166.573 5088 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.01 % Favored : 93.71 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4612 helix: 0.23 (0.10), residues: 2442 sheet: -1.22 (0.28), residues: 325 loop : -2.29 (0.14), residues: 1845 *********************** 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 937 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 931 time to evaluate : 4.379 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 outliers start: 6 outliers final: 2 residues processed: 934 average time/residue: 0.4496 time to fit residues: 702.6593 Evaluate side-chains 673 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 671 time to evaluate : 4.260 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3271 time to fit residues: 6.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 410 optimal weight: 8.9990 chunk 312 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 279 optimal weight: 8.9990 chunk 417 optimal weight: 4.9990 chunk 441 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 119 optimal weight: 0.1980 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 661 GLN ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 120 ASN 9 46 HIS ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.259 37052 Z= 0.781 Angle : 2.278 50.884 50464 Z= 1.481 Chirality : 0.445 6.507 5664 Planarity : 0.006 0.073 6374 Dihedral : 6.670 179.182 5088 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.79 % Favored : 93.91 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.12), residues: 4612 helix: 0.37 (0.10), residues: 2416 sheet: -1.05 (0.30), residues: 298 loop : -2.14 (0.14), residues: 1898 *********************** 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 874 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 872 time to evaluate : 4.270 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 874 average time/residue: 0.4655 time to fit residues: 689.8292 Evaluate side-chains 653 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 653 time to evaluate : 4.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 367 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 328 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 376 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 225 optimal weight: 0.5980 chunk 396 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 330 HIS 4 389 GLN ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS L 582 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN H 183 ASN ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.267 37052 Z= 0.792 Angle : 2.284 50.986 50464 Z= 1.484 Chirality : 0.444 6.464 5664 Planarity : 0.006 0.083 6374 Dihedral : 6.681 176.842 5088 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.37 % Favored : 93.32 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 4612 helix: 0.33 (0.10), residues: 2427 sheet: -1.16 (0.30), residues: 301 loop : -2.12 (0.14), residues: 1884 *********************** 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 824 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 822 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 823 average time/residue: 0.4377 time to fit residues: 608.0358 Evaluate side-chains 610 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 609 time to evaluate : 4.154 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3696 time to fit residues: 6.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 148 optimal weight: 0.5980 chunk 397 optimal weight: 0.0670 chunk 87 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 442 optimal weight: 0.8980 chunk 367 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 369 ASN 1 420 GLN ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN ** 3 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 733 GLN ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 92 HIS K 36 ASN L 582 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.262 37052 Z= 0.769 Angle : 2.253 51.007 50464 Z= 1.470 Chirality : 0.444 6.501 5664 Planarity : 0.005 0.075 6374 Dihedral : 6.321 171.288 5088 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.94 % Favored : 94.77 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4612 helix: 0.56 (0.11), residues: 2414 sheet: -0.96 (0.30), residues: 292 loop : -1.95 (0.14), residues: 1906 *********************** 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 879 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 876 time to evaluate : 4.010 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 outliers start: 3 outliers final: 1 residues processed: 878 average time/residue: 0.4419 time to fit residues: 655.2793 Evaluate side-chains 653 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 652 time to evaluate : 4.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3991 time to fit residues: 6.2894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 426 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 372 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 440 optimal weight: 2.9990 chunk 275 optimal weight: 7.9990 chunk 268 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 3 225 ASN ** 3 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 389 GLN 7 92 HIS K 36 ASN ** L 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN H 226 GLN H 304 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.355 37052 Z= 0.802 Angle : 2.289 50.894 50464 Z= 1.486 Chirality : 0.444 6.451 5664 Planarity : 0.006 0.110 6374 Dihedral : 6.453 172.231 5088 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.40 % Favored : 93.34 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4612 helix: 0.49 (0.10), residues: 2421 sheet: -1.11 (0.31), residues: 273 loop : -1.99 (0.14), residues: 1918 *********************** 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 807 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 806 time to evaluate : 4.735 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 outliers start: 1 outliers final: 0 residues processed: 807 average time/residue: 0.4749 time to fit residues: 648.2727 Evaluate side-chains 620 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 4.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 272 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 346 optimal weight: 0.6980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 147 GLN ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 HIS 3 225 ASN ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 92 HIS K 36 ASN ** L 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.467 37052 Z= 0.787 Angle : 2.290 50.850 50464 Z= 1.484 Chirality : 0.444 6.481 5664 Planarity : 0.006 0.084 6374 Dihedral : 6.455 173.741 5088 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.07 % Favored : 93.67 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4612 helix: 0.52 (0.11), residues: 2404 sheet: -1.05 (0.32), residues: 254 loop : -2.01 (0.14), residues: 1954 *********************** 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 807 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 806 time to evaluate : 4.431 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 outliers start: 1 outliers final: 0 residues processed: 806 average time/residue: 0.4600 time to fit residues: 625.5071 Evaluate side-chains 625 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 4.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 400 optimal weight: 0.9990 chunk 421 optimal weight: 3.9990 chunk 385 optimal weight: 8.9990 chunk 410 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 322 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 370 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 409 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 147 GLN ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 HIS ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 92 HIS K 36 ASN L 325 HIS L 582 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.259 37052 Z= 0.769 Angle : 2.260 50.868 50464 Z= 1.472 Chirality : 0.444 6.495 5664 Planarity : 0.006 0.081 6374 Dihedral : 6.340 177.226 5088 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.66 % Favored : 94.08 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4612 helix: 0.57 (0.11), residues: 2407 sheet: -1.17 (0.31), residues: 270 loop : -1.91 (0.14), residues: 1935 *********************** 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 818 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 816 time to evaluate : 4.014 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 outliers start: 2 outliers final: 1 residues processed: 816 average time/residue: 0.4702 time to fit residues: 650.9788 Evaluate side-chains 637 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 636 time to evaluate : 4.211 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5155 time to fit residues: 6.5139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 269 optimal weight: 0.7980 chunk 434 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 419 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 147 GLN ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN 3 591 HIS ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 92 HIS K 36 ASN L 325 HIS L 582 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.871 37052 Z= 0.877 Angle : 2.332 106.099 50464 Z= 1.490 Chirality : 0.444 6.626 5664 Planarity : 0.006 0.156 6374 Dihedral : 6.324 177.270 5088 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.64 % Favored : 94.12 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4612 helix: 0.58 (0.11), residues: 2406 sheet: -1.16 (0.31), residues: 270 loop : -1.90 (0.14), residues: 1936 ********************** 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 786 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 785 time to evaluate : 4.143 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 outliers start: 1 outliers final: 0 residues processed: 785 average time/residue: 0.4608 time to fit residues: 616.3843 Evaluate side-chains 634 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 4.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 287 optimal weight: 0.8980 chunk 386 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 334 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 372 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 147 GLN ** 1 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN ** 4 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 92 HIS K 36 ASN L 325 HIS ** L 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 GLN ** 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 = 0.3415 r_free = 0.3415 target = 0.104462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092444 restraints weight = 97615.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093857 restraints weight = 63513.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095656 restraints weight = 44700.974| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.871 37052 Z= 0.877 Angle : 2.332 106.099 50464 Z= 1.490 Chirality : 0.444 6.626 5664 Planarity : 0.006 0.156 6374 Dihedral : 6.324 177.270 5088 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.64 % Favored : 94.12 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4612 helix: 0.58 (0.11), residues: 2406 sheet: -1.16 (0.31), residues: 270 loop : -1.90 (0.14), residues: 1936 =============================================================================== Job complete usr+sys time: 10438.34 seconds wall clock time: 187 minutes 28.41 seconds (11248.41 seconds total)