Starting phenix.real_space_refine on Tue Nov 19 10:41:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qma_18496/11_2024/8qma_18496.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qma_18496/11_2024/8qma_18496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qma_18496/11_2024/8qma_18496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qma_18496/11_2024/8qma_18496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qma_18496/11_2024/8qma_18496.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qma_18496/11_2024/8qma_18496.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 S 246 5.16 5 C 33222 2.51 5 N 9000 2.21 5 O 9593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 52064 Number of models: 1 Model: "" Number of chains: 23 Chain: "G" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1766 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "H" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1892 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 14, 'TRANS': 209} Chain: "K" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1681 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 184} Chain: "L" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1801 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 13, 'TRANS': 208} Chain: "M" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "N" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 867 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1538 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain: "P" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "R" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 852 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "S" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3104 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 359} Chain: "A" Number of atoms: 6310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6310 Classifications: {'peptide': 789} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 752} Chain breaks: 7 Chain: "B" Number of atoms: 7445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7445 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 898} Chain breaks: 14 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1666 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 200} Chain breaks: 2 Chain: "D" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2249 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain breaks: 2 Chain: "E" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5075 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 26, 'TRANS': 605} Chain breaks: 3 Chain: "F" Number of atoms: 4060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 4060 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 2645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2645 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 320} Chain breaks: 1 Chain: "J" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3477 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 28, 'TRANS': 397} Chain breaks: 2 Chain: "T" Number of atoms: 4151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4151 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 481} Chain breaks: 10 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22917 SG CYS B 220 77.749 126.002 82.531 1.00106.42 S ATOM 23421 SG CYS B 293 75.925 123.818 85.018 1.00113.25 S ATOM 23479 SG CYS B 300 76.099 123.001 81.244 1.00104.50 S ATOM 23504 SG CYS B 303 78.990 122.315 83.199 1.00105.93 S Time building chain proxies: 26.51, per 1000 atoms: 0.51 Number of scatterers: 52064 At special positions: 0 Unit cell: (141.75, 214.2, 238.35, 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) Zn 1 29.99 Fe 2 26.01 S 246 16.00 O 9593 8.00 N 9000 7.00 C 33222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 107 " - pdb=" SG CYS N 110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.56 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1401 " pdb="ZN ZN B1401 " - pdb=" SG CYS B 300 " pdb="ZN ZN B1401 " - pdb=" SG CYS B 303 " pdb="ZN ZN B1401 " - pdb=" SG CYS B 220 " pdb="ZN ZN B1401 " - pdb=" SG CYS B 293 " Number of angles added : 6 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12076 Finding SS restraints... Secondary structure from input PDB file: 279 helices and 56 sheets defined 47.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.45 Creating SS restraints... Processing helix chain 'G' and resid 68 through 78 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 94 through 100 removed outlier: 3.634A pdb=" N TYR G 100 " --> pdb=" O LYS G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 111 removed outlier: 3.616A pdb=" N ASN G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 118 through 135 removed outlier: 3.591A pdb=" N GLU G 133 " --> pdb=" O ASP G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 155 removed outlier: 3.617A pdb=" N LEU G 148 " --> pdb=" O GLN G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 172 Processing helix chain 'G' and resid 199 through 204 Processing helix chain 'G' and resid 214 through 217 Processing helix chain 'G' and resid 218 through 223 Processing helix chain 'G' and resid 225 through 237 removed outlier: 3.644A pdb=" N TYR G 229 " --> pdb=" O GLU G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 251 Processing helix chain 'H' and resid 234 through 238 removed outlier: 3.739A pdb=" N ARG H 238 " --> pdb=" O TRP H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 266 Processing helix chain 'H' and resid 277 through 313 removed outlier: 6.162A pdb=" N HIS H 289 " --> pdb=" O ARG H 285 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU H 290 " --> pdb=" O ALA H 286 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE H 291 " --> pdb=" O ARG H 287 " (cutoff:3.500A) Proline residue: H 308 - end of helix Processing helix chain 'H' and resid 314 through 316 No H-bonds generated for 'chain 'H' and resid 314 through 316' Processing helix chain 'H' and resid 324 through 336 removed outlier: 4.066A pdb=" N GLU H 334 " --> pdb=" O LYS H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 349 Processing helix chain 'H' and resid 351 through 359 Processing helix chain 'H' and resid 360 through 362 No H-bonds generated for 'chain 'H' and resid 360 through 362' Processing helix chain 'H' and resid 375 through 380 Processing helix chain 'H' and resid 390 through 393 Processing helix chain 'H' and resid 415 through 423 Processing helix chain 'K' and resid 234 through 236 No H-bonds generated for 'chain 'K' and resid 234 through 236' Processing helix chain 'K' and resid 271 through 275 removed outlier: 3.971A pdb=" N ARG K 275 " --> pdb=" O GLY K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 278 No H-bonds generated for 'chain 'K' and resid 276 through 278' Processing helix chain 'K' and resid 301 through 323 removed outlier: 3.927A pdb=" N GLU K 316 " --> pdb=" O THR K 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 331 removed outlier: 6.521A pdb=" N ASP K 327 " --> pdb=" O LYS K 324 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER K 329 " --> pdb=" O ARG K 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 75 Processing helix chain 'L' and resid 75 through 89 Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 113 through 131 removed outlier: 4.688A pdb=" N ASN L 117 " --> pdb=" O PRO L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 151 Processing helix chain 'L' and resid 153 through 167 Processing helix chain 'L' and resid 210 through 215 Processing helix chain 'L' and resid 225 through 228 Processing helix chain 'L' and resid 229 through 234 Processing helix chain 'L' and resid 236 through 248 Processing helix chain 'L' and resid 250 through 267 Processing helix chain 'M' and resid 82 through 92 Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.751A pdb=" N ILE M 111 " --> pdb=" O CYS M 107 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU M 112 " --> pdb=" O GLY M 108 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN M 115 " --> pdb=" O ILE M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 128 No H-bonds generated for 'chain 'M' and resid 126 through 128' Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 172 through 183 Processing helix chain 'N' and resid 82 through 92 Processing helix chain 'N' and resid 108 through 125 removed outlier: 3.752A pdb=" N LEU N 112 " --> pdb=" O GLY N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 145 Processing helix chain 'N' and resid 172 through 181 removed outlier: 3.737A pdb=" N ILE N 179 " --> pdb=" O MET N 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 595 through 609 removed outlier: 3.810A pdb=" N ARG O 601 " --> pdb=" O ASP O 597 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU O 609 " --> pdb=" O SER O 605 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 640 removed outlier: 4.338A pdb=" N VAL O 631 " --> pdb=" O GLY O 627 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR O 633 " --> pdb=" O ARG O 629 " (cutoff:3.500A) Processing helix chain 'O' and resid 654 through 664 Processing helix chain 'O' and resid 665 through 667 No H-bonds generated for 'chain 'O' and resid 665 through 667' Processing helix chain 'O' and resid 669 through 679 Processing helix chain 'O' and resid 696 through 707 Processing helix chain 'O' and resid 735 through 742 removed outlier: 4.676A pdb=" N GLU O 742 " --> pdb=" O GLU O 738 " (cutoff:3.500A) Processing helix chain 'O' and resid 742 through 747 removed outlier: 3.582A pdb=" N TYR O 746 " --> pdb=" O GLU O 742 " (cutoff:3.500A) Processing helix chain 'O' and resid 747 through 753 removed outlier: 4.047A pdb=" N HIS O 751 " --> pdb=" O VAL O 747 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 93 removed outlier: 3.723A pdb=" N ASP P 85 " --> pdb=" O VAL P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 114 Processing helix chain 'P' and resid 123 through 136 Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 54 through 62 removed outlier: 3.887A pdb=" N GLU R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 66 Processing helix chain 'S' and resid 118 through 122 removed outlier: 3.537A pdb=" N GLN S 121 " --> pdb=" O ILE S 118 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP S 122 " --> pdb=" O TYR S 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 118 through 122' Processing helix chain 'S' and resid 123 through 128 Processing helix chain 'S' and resid 139 through 150 removed outlier: 3.610A pdb=" N VAL S 143 " --> pdb=" O PRO S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 176 Processing helix chain 'S' and resid 213 through 217 Processing helix chain 'S' and resid 219 through 223 removed outlier: 3.850A pdb=" N LEU S 223 " --> pdb=" O ALA S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 224 through 231 Processing helix chain 'S' and resid 239 through 242 Processing helix chain 'S' and resid 243 through 260 Processing helix chain 'S' and resid 271 through 276 removed outlier: 3.567A pdb=" N ARG S 276 " --> pdb=" O PRO S 273 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 285 removed outlier: 3.978A pdb=" N LYS S 283 " --> pdb=" O ASN S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 285 through 292 Processing helix chain 'S' and resid 299 through 306 Processing helix chain 'S' and resid 307 through 317 Processing helix chain 'S' and resid 326 through 331 removed outlier: 3.964A pdb=" N ASN S 331 " --> pdb=" O GLN S 328 " (cutoff:3.500A) Processing helix chain 'S' and resid 339 through 344 Processing helix chain 'S' and resid 391 through 407 removed outlier: 3.770A pdb=" N THR S 406 " --> pdb=" O ARG S 402 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 412 Processing helix chain 'S' and resid 413 through 432 removed outlier: 4.015A pdb=" N PHE S 423 " --> pdb=" O ARG S 419 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA S 424 " --> pdb=" O GLN S 420 " (cutoff:3.500A) Processing helix chain 'S' and resid 443 through 455 Processing helix chain 'S' and resid 456 through 460 Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.706A pdb=" N LYS A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.692A pdb=" N TYR A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 200 through 206 removed outlier: 3.513A pdb=" N PHE A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.538A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 316 through 346 Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.690A pdb=" N ILE A 387 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 535 through 540 removed outlier: 6.180A pdb=" N ASP A 540 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 4.233A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 578 removed outlier: 4.323A pdb=" N GLN A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 865 through 881 Processing helix chain 'A' and resid 889 through 893 Processing helix chain 'A' and resid 896 through 914 Processing helix chain 'A' and resid 988 through 998 Processing helix chain 'A' and resid 1000 through 1009 removed outlier: 3.527A pdb=" N LEU A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1051 Processing helix chain 'B' and resid 15 through 31 Processing helix chain 'B' and resid 31 through 53 removed outlier: 3.662A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 88 Processing helix chain 'B' and resid 92 through 114 removed outlier: 4.227A pdb=" N TRP B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.615A pdb=" N ASN B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 174 through 211 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.694A pdb=" N VAL B 369 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 removed outlier: 3.993A pdb=" N GLU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 999 through 1007 removed outlier: 3.921A pdb=" N ILE B1004 " --> pdb=" O GLN B1000 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1013 removed outlier: 3.611A pdb=" N PHE B1012 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS B1013 " --> pdb=" O ASP B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1156 removed outlier: 3.688A pdb=" N GLU B1154 " --> pdb=" O GLU B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1212 removed outlier: 3.919A pdb=" N GLY B1171 " --> pdb=" O LYS B1167 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N THR B1177 " --> pdb=" O ASN B1173 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ARG B1178 " --> pdb=" O ARG B1174 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B1182 " --> pdb=" O ARG B1178 " (cutoff:3.500A) Proline residue: B1183 - end of helix removed outlier: 4.808A pdb=" N PHE B1186 " --> pdb=" O ILE B1182 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B1187 " --> pdb=" O PRO B1183 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B1208 " --> pdb=" O LYS B1204 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B1209 " --> pdb=" O ILE B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1229 removed outlier: 3.942A pdb=" N ILE B1221 " --> pdb=" O HIS B1217 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B1223 " --> pdb=" O ARG B1219 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B1224 " --> pdb=" O HIS B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1239 Processing helix chain 'B' and resid 1251 through 1261 Processing helix chain 'B' and resid 1273 through 1278 Processing helix chain 'B' and resid 1283 through 1289 removed outlier: 3.541A pdb=" N GLU B1287 " --> pdb=" O SER B1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1303 Processing helix chain 'B' and resid 1312 through 1317 removed outlier: 3.888A pdb=" N VAL B1317 " --> pdb=" O LYS B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1329 removed outlier: 4.584A pdb=" N ASN B1329 " --> pdb=" O THR B1326 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 56 removed outlier: 3.679A pdb=" N THR C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.806A pdb=" N GLU C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 227 Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.719A pdb=" N THR D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 210 through 227 Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.855A pdb=" N GLU D 235 " --> pdb=" O VAL D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.682A pdb=" N CYS D 286 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'E' and resid 65 through 84 Processing helix chain 'E' and resid 86 through 100 Processing helix chain 'E' and resid 105 through 119 removed outlier: 3.543A pdb=" N PHE E 109 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 135 Processing helix chain 'E' and resid 140 through 155 removed outlier: 3.848A pdb=" N MET E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 168 through 171 Processing helix chain 'E' and resid 173 through 188 removed outlier: 4.543A pdb=" N ALA E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 209 through 223 Processing helix chain 'E' and resid 225 through 239 removed outlier: 4.281A pdb=" N ASP E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.630A pdb=" N VAL E 254 " --> pdb=" O CYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'E' and resid 260 through 273 removed outlier: 4.215A pdb=" N ALA E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR E 267 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 281 through 294 Processing helix chain 'E' and resid 300 through 314 Processing helix chain 'E' and resid 321 through 335 Processing helix chain 'E' and resid 337 through 349 removed outlier: 4.279A pdb=" N ARG E 343 " --> pdb=" O LYS E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 366 through 378 Processing helix chain 'E' and resid 380 through 395 removed outlier: 4.145A pdb=" N ASP E 386 " --> pdb=" O VAL E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 404 removed outlier: 3.973A pdb=" N ILE E 404 " --> pdb=" O ARG E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 436 Processing helix chain 'E' and resid 474 through 498 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 506 through 522 Processing helix chain 'E' and resid 593 through 601 Processing helix chain 'E' and resid 610 through 615 Processing helix chain 'E' and resid 744 through 755 Processing helix chain 'E' and resid 759 through 763 Processing helix chain 'E' and resid 765 through 770 Processing helix chain 'E' and resid 772 through 774 No H-bonds generated for 'chain 'E' and resid 772 through 774' Processing helix chain 'E' and resid 775 through 780 removed outlier: 4.469A pdb=" N ASN E 780 " --> pdb=" O LYS E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 805 Processing helix chain 'E' and resid 810 through 824 Processing helix chain 'E' and resid 827 through 840 removed outlier: 4.027A pdb=" N LEU E 831 " --> pdb=" O PRO E 827 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS E 832 " --> pdb=" O SER E 828 " (cutoff:3.500A) Processing helix chain 'E' and resid 845 through 860 removed outlier: 3.762A pdb=" N TYR E 849 " --> pdb=" O GLY E 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 876 Processing helix chain 'E' and resid 880 through 889 removed outlier: 5.745A pdb=" N LYS E 886 " --> pdb=" O GLN E 882 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL E 887 " --> pdb=" O THR E 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 892 No H-bonds generated for 'chain 'E' and resid 890 through 892' Processing helix chain 'F' and resid 68 through 78 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 109 through 119 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'F' and resid 134 through 142 Processing helix chain 'F' and resid 179 through 188 Processing helix chain 'F' and resid 189 through 195 Processing helix chain 'F' and resid 198 through 203 removed outlier: 4.659A pdb=" N ASP F 203 " --> pdb=" O LEU F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 217 removed outlier: 6.825A pdb=" N VAL F 214 " --> pdb=" O ASP F 211 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP F 215 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 248 removed outlier: 5.890A pdb=" N ASP F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 309 through 317 removed outlier: 5.076A pdb=" N HIS F 315 " --> pdb=" O PHE F 311 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE F 316 " --> pdb=" O TRP F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 391 through 395 removed outlier: 3.678A pdb=" N GLU F 395 " --> pdb=" O PRO F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 422 removed outlier: 4.410A pdb=" N LYS F 406 " --> pdb=" O PRO F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 428 Processing helix chain 'F' and resid 432 through 436 Processing helix chain 'F' and resid 468 through 472 Processing helix chain 'F' and resid 473 through 495 Processing helix chain 'F' and resid 503 through 538 Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 249 through 260 Processing helix chain 'I' and resid 273 through 286 Processing helix chain 'I' and resid 322 through 326 Processing helix chain 'I' and resid 328 through 332 removed outlier: 3.712A pdb=" N ILE I 332 " --> pdb=" O LYS I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 339 removed outlier: 3.775A pdb=" N GLU I 339 " --> pdb=" O ASP I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 351 removed outlier: 3.683A pdb=" N LEU I 351 " --> pdb=" O HIS I 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 348 through 351' Processing helix chain 'I' and resid 352 through 370 Processing helix chain 'I' and resid 380 through 384 removed outlier: 3.740A pdb=" N TRP I 384 " --> pdb=" O LEU I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 399 removed outlier: 5.178A pdb=" N GLU I 396 " --> pdb=" O SER I 392 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL I 397 " --> pdb=" O LEU I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 416 Processing helix chain 'I' and resid 437 through 442 removed outlier: 3.886A pdb=" N VAL I 441 " --> pdb=" O GLU I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 443 through 445 No H-bonds generated for 'chain 'I' and resid 443 through 445' Processing helix chain 'I' and resid 487 through 505 removed outlier: 3.514A pdb=" N GLY I 491 " --> pdb=" O MET I 487 " (cutoff:3.500A) Processing helix chain 'I' and resid 506 through 509 Processing helix chain 'I' and resid 511 through 538 Processing helix chain 'J' and resid 63 through 67 removed outlier: 4.201A pdb=" N GLU J 66 " --> pdb=" O ALA J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 85 removed outlier: 3.951A pdb=" N TYR J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY J 83 " --> pdb=" O PHE J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 127 No H-bonds generated for 'chain 'J' and resid 125 through 127' Processing helix chain 'J' and resid 147 through 155 removed outlier: 3.878A pdb=" N ASP J 151 " --> pdb=" O HIS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 176 Processing helix chain 'J' and resid 179 through 185 removed outlier: 4.002A pdb=" N LEU J 183 " --> pdb=" O HIS J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 188 No H-bonds generated for 'chain 'J' and resid 186 through 188' Processing helix chain 'J' and resid 196 through 200 Processing helix chain 'J' and resid 201 through 209 removed outlier: 4.138A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 232 Processing helix chain 'J' and resid 237 through 242 Processing helix chain 'J' and resid 246 through 261 removed outlier: 3.616A pdb=" N PHE J 250 " --> pdb=" O ASP J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 336 Processing helix chain 'J' and resid 359 through 366 removed outlier: 3.515A pdb=" N PHE J 366 " --> pdb=" O PHE J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 399 Processing helix chain 'J' and resid 410 through 431 removed outlier: 3.603A pdb=" N ARG J 415 " --> pdb=" O PRO J 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 445 removed outlier: 3.758A pdb=" N ASP J 439 " --> pdb=" O THR J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 481 Processing helix chain 'T' and resid 16 through 23 Processing helix chain 'T' and resid 115 through 120 Processing helix chain 'T' and resid 124 through 131 Processing helix chain 'T' and resid 133 through 140 Processing helix chain 'T' and resid 174 through 179 Processing helix chain 'T' and resid 180 through 192 removed outlier: 4.337A pdb=" N ILE T 186 " --> pdb=" O GLN T 182 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN T 189 " --> pdb=" O GLU T 185 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG T 190 " --> pdb=" O ILE T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 205 removed outlier: 3.817A pdb=" N ILE T 199 " --> pdb=" O GLY T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 207 through 225 removed outlier: 3.645A pdb=" N ILE T 212 " --> pdb=" O LEU T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 255 Processing helix chain 'T' and resid 260 through 263 Processing helix chain 'T' and resid 273 through 277 Processing helix chain 'T' and resid 292 through 312 Processing helix chain 'T' and resid 319 through 337 Processing helix chain 'T' and resid 356 through 360 Processing helix chain 'T' and resid 366 through 370 Processing helix chain 'T' and resid 399 through 406 removed outlier: 4.343A pdb=" N GLU T 404 " --> pdb=" O GLU T 400 " (cutoff:3.500A) Processing helix chain 'T' and resid 406 through 417 Processing helix chain 'T' and resid 422 through 433 Processing helix chain 'T' and resid 434 through 446 removed outlier: 3.633A pdb=" N TRP T 438 " --> pdb=" O LYS T 434 " (cutoff:3.500A) Processing helix chain 'T' and resid 502 through 513 Processing helix chain 'T' and resid 514 through 518 Processing helix chain 'T' and resid 533 through 545 removed outlier: 3.792A pdb=" N GLY T 545 " --> pdb=" O VAL T 541 " (cutoff:3.500A) Processing helix chain 'T' and resid 548 through 552 Processing helix chain 'T' and resid 583 through 593 Processing helix chain 'T' and resid 656 through 674 removed outlier: 3.570A pdb=" N ILE T 665 " --> pdb=" O PHE T 661 " (cutoff:3.500A) Processing helix chain 'T' and resid 675 through 677 No H-bonds generated for 'chain 'T' and resid 675 through 677' Processing sheet with id=AA1, first strand: chain 'G' and resid 189 through 195 removed outlier: 7.251A pdb=" N GLY G 176 " --> pdb=" O ASP G 212 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASP G 212 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL G 178 " --> pdb=" O SER G 210 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER G 210 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU G 180 " --> pdb=" O ILE G 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 395 through 396 Processing sheet with id=AA3, first strand: chain 'H' and resid 426 through 427 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 426 through 427 current: chain 'A' and resid 49 through 60 removed outlier: 4.562A pdb=" N SER A 83 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLU A 55 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N TYR A 81 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N TYR A 57 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N GLU A 79 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU A 59 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N SER A 77 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 82 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE A 100 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA A 84 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 98 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 141 through 145 Processing sheet with id=AA5, first strand: chain 'K' and resid 163 through 164 removed outlier: 6.102A pdb=" N ARG K 194 " --> pdb=" O HIS K 232 " (cutoff:3.500A) removed outlier: 10.559A pdb=" N VAL K 227 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N ILE K 250 " --> pdb=" O VAL K 227 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N LEU K 229 " --> pdb=" O GLU K 248 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N GLU K 248 " --> pdb=" O LEU K 229 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS K 231 " --> pdb=" O ASP K 246 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG K 183 " --> pdb=" O ILE K 260 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ARG K 262 " --> pdb=" O ARG K 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 202 through 205 Processing sheet with id=AA7, first strand: chain 'K' and resid 266 through 267 removed outlier: 6.850A pdb=" N LEU K 266 " --> pdb=" O ILE K 293 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N HIS K 295 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN T 629 " --> pdb=" O GLU T 625 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR T 649 " --> pdb=" O VAL T 640 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER T 642 " --> pdb=" O THR T 647 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR T 647 " --> pdb=" O SER T 642 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE T 650 " --> pdb=" O TRP T 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 200 through 206 removed outlier: 7.126A pdb=" N GLY L 172 " --> pdb=" O ASP L 223 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP L 223 " --> pdb=" O GLY L 172 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR L 174 " --> pdb=" O THR L 221 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR L 221 " --> pdb=" O THR L 174 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU L 176 " --> pdb=" O LEU L 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 79 through 80 removed outlier: 6.250A pdb=" N ARG M 79 " --> pdb=" O LYS M 132 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE M 99 " --> pdb=" O VAL M 131 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG S 195 " --> pdb=" O VAL S 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 79 through 80 removed outlier: 6.042A pdb=" N ARG N 79 " --> pdb=" O LYS N 132 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP N 134 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE N 99 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL N 133 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP N 101 " --> pdb=" O VAL N 133 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR N 152 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE N 165 " --> pdb=" O PHE N 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 578 through 579 removed outlier: 6.082A pdb=" N ILE O 615 " --> pdb=" O VAL O 715 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA O 717 " --> pdb=" O ILE O 615 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL O 617 " --> pdb=" O ALA O 717 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE O 614 " --> pdb=" O VAL O 642 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N MET O 644 " --> pdb=" O ILE O 614 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR O 616 " --> pdb=" O MET O 644 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR O 646 " --> pdb=" O THR O 616 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE O 618 " --> pdb=" O THR O 646 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 724 through 727 removed outlier: 3.622A pdb=" N LYS O 730 " --> pdb=" O GLU O 727 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 48 through 50 removed outlier: 3.663A pdb=" N LYS R 48 " --> pdb=" O ARG R 113 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP R 83 " --> pdb=" O LYS R 135 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER R 129 " --> pdb=" O GLU R 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 74 through 79 Processing sheet with id=AB6, first strand: chain 'S' and resid 179 through 186 removed outlier: 6.865A pdb=" N ALA S 154 " --> pdb=" O GLN S 179 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ARG S 181 " --> pdb=" O ALA S 154 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N PHE S 156 " --> pdb=" O ARG S 181 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL S 183 " --> pdb=" O PHE S 156 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY S 158 " --> pdb=" O VAL S 183 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE S 185 " --> pdb=" O GLY S 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL S 160 " --> pdb=" O PHE S 185 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL S 93 " --> pdb=" O ALA S 155 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET S 157 " --> pdb=" O VAL S 93 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS S 95 " --> pdb=" O MET S 157 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LYS S 159 " --> pdb=" O CYS S 95 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY S 97 " --> pdb=" O LYS S 159 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N GLY S 161 " --> pdb=" O GLY S 97 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU S 92 " --> pdb=" O ILE S 233 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N HIS S 235 " --> pdb=" O LEU S 92 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS S 94 " --> pdb=" O HIS S 235 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ASN S 237 " --> pdb=" O CYS S 94 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N PHE S 96 " --> pdb=" O ASN S 237 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE S 264 " --> pdb=" O ILE S 294 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU S 296 " --> pdb=" O ILE S 264 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE S 266 " --> pdb=" O GLU S 296 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER S 298 " --> pdb=" O PHE S 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AB8, first strand: chain 'A' and resid 312 through 315 removed outlier: 6.443A pdb=" N ASN A 124 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 131 through 137 removed outlier: 13.076A pdb=" N ARG A 157 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N SER A 173 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 159 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 443 through 444 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 468 through 471 current: chain 'A' and resid 498 through 503 Processing sheet with id=AC2, first strand: chain 'A' and resid 581 through 582 removed outlier: 6.609A pdb=" N ALA A 581 " --> pdb=" O LEU A 640 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 604 through 609 removed outlier: 6.796A pdb=" N LYS A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 592 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 598 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AC5, first strand: chain 'A' and resid 655 through 656 removed outlier: 7.189A pdb=" N VAL A 673 " --> pdb=" O SER A 833 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 835 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 675 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 674 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A 943 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1067 through 1069 removed outlier: 4.568A pdb=" N HIS T 7 " --> pdb=" O VAL A1060 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 215 through 217 removed outlier: 7.662A pdb=" N ILE B 299 " --> pdb=" O ARG B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AC9, first strand: chain 'B' and resid 255 through 257 removed outlier: 6.563A pdb=" N ILE B 255 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.653A pdb=" N VAL B 354 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 397 through 402 Processing sheet with id=AD3, first strand: chain 'B' and resid 436 through 443 removed outlier: 6.561A pdb=" N GLU B 436 " --> pdb=" O GLU B1135 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU B1135 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL B 438 " --> pdb=" O ILE B1133 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE B1133 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS B 440 " --> pdb=" O THR B1131 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B1131 " --> pdb=" O LYS B 440 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 442 " --> pdb=" O LEU B1129 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B1129 " --> pdb=" O HIS B1116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 448 through 451 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 474 through 480 current: chain 'B' and resid 1030 through 1031 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1030 through 1031 current: chain 'B' and resid 1089 through 1095 removed outlier: 6.510A pdb=" N VAL B1100 " --> pdb=" O LEU B1092 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1099 through 1109 current: chain 'F' and resid 290 through 294 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 301 through 304 current: chain 'F' and resid 340 through 344 Processing sheet with id=AD5, first strand: chain 'B' and resid 499 through 500 removed outlier: 6.643A pdb=" N GLN B 499 " --> pdb=" O HIS F 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 571 through 573 removed outlier: 3.664A pdb=" N ARG B 576 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP B 870 " --> pdb=" O PHE B 581 " (cutoff:3.500A) removed outlier: 14.541A pdb=" N LYS F 459 " --> pdb=" O VAL B 855 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ALA B 857 " --> pdb=" O LYS F 459 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 600 through 601 removed outlier: 6.752A pdb=" N LEU B 839 " --> pdb=" O PHE B 615 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 924 through 928 Processing sheet with id=AD9, first strand: chain 'B' and resid 997 through 998 Processing sheet with id=AE1, first strand: chain 'B' and resid 1039 through 1041 Processing sheet with id=AE2, first strand: chain 'B' and resid 1248 through 1250 Processing sheet with id=AE3, first strand: chain 'C' and resid 14 through 24 removed outlier: 6.619A pdb=" N ARG C 31 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER C 20 " --> pdb=" O TYR C 29 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 29 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG C 22 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 27 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR C 29 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 205 " --> pdb=" O TYR C 29 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG C 31 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE C 203 " --> pdb=" O ARG C 31 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE C 33 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 201 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N SER C 35 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU C 199 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 181 " --> pdb=" O TRP C 204 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.458A pdb=" N GLY C 148 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA C 65 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 150 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 152 " --> pdb=" O CYS C 61 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AE6, first strand: chain 'C' and resid 114 through 117 Processing sheet with id=AE7, first strand: chain 'D' and resid 14 through 24 removed outlier: 6.030A pdb=" N TRP D 15 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER D 35 " --> pdb=" O TRP D 15 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N CYS D 17 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE D 33 " --> pdb=" O CYS D 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR D 29 " --> pdb=" O THR D 205 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR D 205 " --> pdb=" O TYR D 29 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ARG D 31 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE D 203 " --> pdb=" O ARG D 31 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE D 33 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 201 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER D 35 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU D 199 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 103 through 110 removed outlier: 7.900A pdb=" N CYS D 146 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER D 67 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY D 148 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA D 65 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS D 150 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 114 through 117 Processing sheet with id=AF1, first strand: chain 'F' and resid 385 through 386 removed outlier: 5.361A pdb=" N ARG F 385 " --> pdb=" O LYS F 548 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'I' and resid 263 through 267 removed outlier: 6.528A pdb=" N VAL I 203 " --> pdb=" O ALA I 265 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N MET I 267 " --> pdb=" O VAL I 203 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS I 205 " --> pdb=" O MET I 267 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU I 202 " --> pdb=" O MET I 342 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR I 344 " --> pdb=" O LEU I 202 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS I 204 " --> pdb=" O TYR I 344 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR I 346 " --> pdb=" O CYS I 204 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE I 206 " --> pdb=" O THR I 346 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE I 404 " --> pdb=" O PHE I 453 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR I 455 " --> pdb=" O ILE I 404 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL I 406 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS I 460 " --> pdb=" O ASN I 456 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 218 through 219 Processing sheet with id=AF4, first strand: chain 'J' and resid 73 through 74 removed outlier: 3.637A pdb=" N GLU J 73 " --> pdb=" O GLU J 97 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 89 through 90 removed outlier: 6.335A pdb=" N VAL J 306 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU J 121 " --> pdb=" O LEU J 304 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU J 304 " --> pdb=" O GLU J 121 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 128 through 131 Processing sheet with id=AF7, first strand: chain 'J' and resid 286 through 287 removed outlier: 6.099A pdb=" N ASN J 286 " --> pdb=" O ILE J 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'J' and resid 357 through 358 removed outlier: 5.818A pdb=" N ILE J 357 " --> pdb=" O TRP J 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'T' and resid 105 through 114 removed outlier: 9.891A pdb=" N LEU T 109 " --> pdb=" O PRO T 270 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N CYS T 111 " --> pdb=" O LEU T 268 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU T 268 " --> pdb=" O CYS T 111 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 385 through 386 removed outlier: 5.845A pdb=" N VAL T 385 " --> pdb=" O LEU T 478 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS T 395 " --> pdb=" O ILE T 469 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL T 471 " --> pdb=" O CYS T 395 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU T 397 " --> pdb=" O VAL T 471 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 520 through 521 2328 hydrogen bonds defined for protein. 6459 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: 23.86 Time building geometry restraints manager: 14.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17122 1.34 - 1.46: 9939 1.46 - 1.58: 25756 1.58 - 1.70: 1 1.70 - 1.81: 409 Bond restraints: 53227 Sorted by residual: bond pdb=" N PRO B1323 " pdb=" CA PRO B1323 " ideal model delta sigma weight residual 1.469 1.443 0.025 7.40e-03 1.83e+04 1.18e+01 bond pdb=" CA PRO B1323 " pdb=" C PRO B1323 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" CA PRO B1323 " pdb=" CB PRO B1323 " ideal model delta sigma weight residual 1.532 1.516 0.016 7.10e-03 1.98e+04 4.86e+00 bond pdb=" CA ALA B1324 " pdb=" CB ALA B1324 " ideal model delta sigma weight residual 1.532 1.500 0.032 1.56e-02 4.11e+03 4.16e+00 bond pdb=" CB PRO H 212 " pdb=" CG PRO H 212 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.83e+00 ... (remaining 53222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.77: 71954 5.77 - 11.54: 38 11.54 - 17.31: 3 17.31 - 23.08: 0 23.08 - 28.86: 1 Bond angle restraints: 71996 Sorted by residual: angle pdb=" C SER D 35 " pdb=" N PRO D 36 " pdb=" CD PRO D 36 " ideal model delta sigma weight residual 125.00 96.14 28.86 4.10e+00 5.95e-02 4.95e+01 angle pdb=" N PRO A 352 " pdb=" CA PRO A 352 " pdb=" C PRO A 352 " ideal model delta sigma weight residual 112.47 100.83 11.64 2.06e+00 2.36e-01 3.19e+01 angle pdb=" N PRO B1323 " pdb=" CA PRO B1323 " pdb=" C PRO B1323 " ideal model delta sigma weight residual 113.70 105.67 8.03 1.76e+00 3.23e-01 2.08e+01 angle pdb=" N GLN A 353 " pdb=" CA GLN A 353 " pdb=" C GLN A 353 " ideal model delta sigma weight residual 110.80 102.02 8.78 2.13e+00 2.20e-01 1.70e+01 angle pdb=" C PRO H 398 " pdb=" N ASP H 399 " pdb=" CA ASP H 399 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.67e+01 ... (remaining 71991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 29513 17.89 - 35.79: 2161 35.79 - 53.68: 347 53.68 - 71.57: 110 71.57 - 89.47: 51 Dihedral angle restraints: 32182 sinusoidal: 13507 harmonic: 18675 Sorted by residual: dihedral pdb=" CD ARG B 195 " pdb=" NE ARG B 195 " pdb=" CZ ARG B 195 " pdb=" NH1 ARG B 195 " ideal model delta sinusoidal sigma weight residual 0.00 87.35 -87.35 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CD ARG L 160 " pdb=" NE ARG L 160 " pdb=" CZ ARG L 160 " pdb=" NH1 ARG L 160 " ideal model delta sinusoidal sigma weight residual 0.00 -81.53 81.53 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CD ARG L 182 " pdb=" NE ARG L 182 " pdb=" CZ ARG L 182 " pdb=" NH1 ARG L 182 " ideal model delta sinusoidal sigma weight residual 0.00 66.42 -66.42 1 1.00e+01 1.00e-02 5.76e+01 ... (remaining 32179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 6793 0.071 - 0.142: 990 0.142 - 0.212: 48 0.212 - 0.283: 2 0.283 - 0.354: 2 Chirality restraints: 7835 Sorted by residual: chirality pdb=" CA PRO D 36 " pdb=" N PRO D 36 " pdb=" C PRO D 36 " pdb=" CB PRO D 36 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA PRO H 212 " pdb=" N PRO H 212 " pdb=" C PRO H 212 " pdb=" CB PRO H 212 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ASP E 459 " pdb=" N ASP E 459 " pdb=" C ASP E 459 " pdb=" CB ASP E 459 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 7832 not shown) Planarity restraints: 9296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 195 " 0.964 9.50e-02 1.11e+02 4.33e-01 1.22e+02 pdb=" NE ARG B 195 " -0.077 2.00e-02 2.50e+03 pdb=" CZ ARG B 195 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG B 195 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 195 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 160 " -0.939 9.50e-02 1.11e+02 4.22e-01 1.18e+02 pdb=" NE ARG L 160 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG L 160 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG L 160 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG L 160 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 182 " 0.833 9.50e-02 1.11e+02 3.75e-01 9.83e+01 pdb=" NE ARG L 182 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG L 182 " 0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG L 182 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG L 182 " 0.001 2.00e-02 2.50e+03 ... (remaining 9293 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 396 2.58 - 3.16: 44753 3.16 - 3.74: 82608 3.74 - 4.32: 119040 4.32 - 4.90: 194048 Nonbonded interactions: 440845 Sorted by model distance: nonbonded pdb=" OD2 ASP L 223 " pdb="FE FE L 500 " model vdw 1.997 2.260 nonbonded pdb=" OD2 ASP G 212 " pdb="FE FE G 500 " model vdw 2.026 2.260 nonbonded pdb=" NE2 HIS L 227 " pdb="FE FE L 500 " model vdw 2.070 2.340 nonbonded pdb=" NE2 HIS G 216 " pdb="FE FE G 500 " model vdw 2.071 2.340 nonbonded pdb=" NE2 HIS L 72 " pdb="FE FE L 500 " model vdw 2.123 2.340 ... (remaining 440840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'M' and resid 77 through 184) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.660 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: 0.050 Extract box with map and model: 1.830 Check model and map are aligned: 0.330 Set scattering table: 0.480 Process input model: 118.340 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 : 0.004 0.098 53227 Z= 0.239 Angle : 0.692 28.856 71996 Z= 0.377 Chirality : 0.048 0.354 7835 Planarity : 0.014 0.433 9296 Dihedral : 13.654 89.468 20103 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.03 % Favored : 95.75 % Rotamer: Outliers : 0.74 % Allowed : 2.17 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.10), residues: 6299 helix: -1.01 (0.09), residues: 2572 sheet: -0.24 (0.17), residues: 823 loop : -0.70 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP L 214 HIS 0.010 0.001 HIS F 346 PHE 0.031 0.002 PHE J 139 TYR 0.031 0.003 TYR F 483 ARG 0.063 0.004 ARG L 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 566 time to evaluate : 6.161 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: G 135 MET cc_start: 0.8073 (mtm) cc_final: 0.7725 (mtm) REVERT: G 204 ASP cc_start: 0.7292 (t0) cc_final: 0.6670 (t0) REVERT: H 346 MET cc_start: 0.8672 (ttp) cc_final: 0.8305 (ttp) REVERT: K 203 TYR cc_start: 0.8605 (m-80) cc_final: 0.8282 (m-80) REVERT: K 287 ASN cc_start: 0.8479 (t0) cc_final: 0.7850 (t0) REVERT: K 290 SER cc_start: 0.8843 (t) cc_final: 0.8479 (m) REVERT: K 329 SER cc_start: 0.8721 (m) cc_final: 0.8507 (t) REVERT: K 334 PHE cc_start: 0.7077 (t80) cc_final: 0.6635 (t80) REVERT: L 108 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7944 (mtp180) REVERT: L 159 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: L 182 ARG cc_start: 0.7782 (ptp90) cc_final: 0.7500 (mtm-85) REVERT: M 184 MET cc_start: 0.6997 (mmp) cc_final: 0.6751 (mmp) REVERT: N 122 VAL cc_start: 0.9251 (p) cc_final: 0.8835 (m) REVERT: O 746 TYR cc_start: 0.6348 (p90) cc_final: 0.5823 (p90) REVERT: P 91 LEU cc_start: 0.8296 (tt) cc_final: 0.8056 (tt) REVERT: P 95 ASN cc_start: 0.7459 (t0) cc_final: 0.7203 (t0) REVERT: P 123 LYS cc_start: 0.7947 (mmmt) cc_final: 0.6918 (mmtt) REVERT: P 128 VAL cc_start: 0.8493 (t) cc_final: 0.8208 (t) REVERT: R 42 GLU cc_start: 0.7915 (pm20) cc_final: 0.7506 (pm20) REVERT: R 50 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7641 (mt-10) REVERT: R 56 ARG cc_start: 0.7786 (tmm160) cc_final: 0.7232 (tmm160) REVERT: R 60 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7637 (mt-10) REVERT: R 101 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8272 (mmtm) REVERT: R 121 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: S 124 MET cc_start: 0.8426 (mtp) cc_final: 0.8065 (mtp) REVERT: S 460 TRP cc_start: 0.8139 (m-10) cc_final: 0.7639 (m-10) REVERT: A 107 MET cc_start: 0.8155 (ttm) cc_final: 0.7932 (ttm) REVERT: A 158 LEU cc_start: 0.6921 (tp) cc_final: 0.6529 (tp) REVERT: A 446 ASP cc_start: 0.7043 (p0) cc_final: 0.6446 (t70) REVERT: A 662 MET cc_start: 0.8248 (ptm) cc_final: 0.7547 (ptm) REVERT: A 1070 LYS cc_start: 0.7039 (tptt) cc_final: 0.6721 (tptt) REVERT: B 7 LEU cc_start: 0.7168 (pt) cc_final: 0.6818 (mp) REVERT: B 182 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7444 (m) REVERT: B 183 TYR cc_start: 0.5232 (OUTLIER) cc_final: 0.4818 (m-10) REVERT: B 803 ARG cc_start: 0.6725 (ttm-80) cc_final: 0.6317 (tpp-160) REVERT: C 66 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8045 (mtpp) REVERT: D 177 MET cc_start: 0.8338 (mtp) cc_final: 0.8130 (mtm) REVERT: E 77 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8130 (pt0) REVERT: E 109 PHE cc_start: 0.7637 (m-80) cc_final: 0.7395 (m-10) REVERT: E 221 CYS cc_start: 0.7553 (m) cc_final: 0.7315 (p) REVERT: E 250 CYS cc_start: 0.8294 (m) cc_final: 0.7612 (m) REVERT: E 310 MET cc_start: 0.8060 (mtm) cc_final: 0.7794 (mtp) REVERT: E 311 MET cc_start: 0.8673 (ttm) cc_final: 0.8397 (ttp) REVERT: E 405 MET cc_start: 0.7225 (mtm) cc_final: 0.6981 (mtp) REVERT: E 407 ARG cc_start: 0.6133 (tpt170) cc_final: 0.5908 (tpt170) REVERT: E 514 MET cc_start: 0.7613 (mtp) cc_final: 0.7201 (mtp) REVERT: E 799 MET cc_start: 0.8580 (ttp) cc_final: 0.8351 (ptp) REVERT: E 826 MET cc_start: 0.8091 (ptm) cc_final: 0.7752 (ptp) REVERT: E 831 LEU cc_start: 0.8569 (tt) cc_final: 0.8237 (pp) REVERT: E 835 GLN cc_start: 0.8453 (mt0) cc_final: 0.8132 (mp10) REVERT: F 386 LYS cc_start: 0.8535 (mttt) cc_final: 0.8051 (mmtt) REVERT: F 424 ASN cc_start: 0.6422 (m-40) cc_final: 0.6181 (t0) REVERT: F 498 TYR cc_start: 0.4597 (t80) cc_final: 0.4255 (t80) REVERT: I 306 MET cc_start: 0.6153 (mmt) cc_final: 0.5795 (mmm) REVERT: I 356 MET cc_start: 0.8254 (tpt) cc_final: 0.7879 (tpt) REVERT: I 445 TRP cc_start: 0.8155 (t-100) cc_final: 0.7920 (t-100) REVERT: J 115 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7724 (mtp-110) REVERT: J 332 MET cc_start: 0.8411 (tpt) cc_final: 0.8124 (tpt) REVERT: J 346 TRP cc_start: 0.8818 (m100) cc_final: 0.8248 (m100) REVERT: J 465 MET cc_start: 0.8195 (tpt) cc_final: 0.7763 (tpt) REVERT: T 431 ARG cc_start: 0.6650 (ttm-80) cc_final: 0.5857 (mtt180) REVERT: T 443 GLU cc_start: 0.6965 (tt0) cc_final: 0.5826 (tm-30) REVERT: T 445 MET cc_start: 0.7042 (ttm) cc_final: 0.6239 (mtp) outliers start: 42 outliers final: 16 residues processed: 605 average time/residue: 0.7494 time to fit residues: 717.6173 Evaluate side-chains 453 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 433 time to evaluate : 6.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 295 HIS Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 196 GLU Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain S residue 129 PRO Chi-restraints excluded: chain S residue 181 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 1163 LEU Chi-restraints excluded: chain D residue 36 PRO Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 535 optimal weight: 1.9990 chunk 480 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 324 optimal weight: 3.9990 chunk 256 optimal weight: 0.0270 chunk 496 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 369 optimal weight: 5.9990 chunk 575 optimal weight: 5.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN H 349 HIS ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 ASN L 187 ASN L 267 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 768 HIS R 105 GLN S 147 HIS S 235 HIS S 432 GLN A 292 HIS A 307 ASN A 465 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 ASN B1196 GLN C 135 HIS C 184 HIS D 69 ASN D 135 HIS ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 ASN E 469 ASN F 370 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 GLN I 229 GLN I 368 GLN I 505 GLN J 273 GLN J 344 ASN J 438 GLN T 128 ASN T 593 GLN T 610 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 53227 Z= 0.345 Angle : 0.656 11.061 71996 Z= 0.344 Chirality : 0.047 0.256 7835 Planarity : 0.005 0.162 9296 Dihedral : 6.517 74.507 7115 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 1.11 % Allowed : 5.77 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.10 (0.10), residues: 6299 helix: 0.39 (0.10), residues: 2611 sheet: -0.18 (0.17), residues: 827 loop : -0.32 (0.12), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 214 HIS 0.015 0.001 HIS F 346 PHE 0.039 0.002 PHE E 830 TYR 0.024 0.002 TYR K 200 ARG 0.009 0.001 ARG G 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 465 time to evaluate : 6.179 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: G 204 ASP cc_start: 0.7413 (t0) cc_final: 0.6834 (t0) REVERT: K 153 ILE cc_start: 0.8412 (mm) cc_final: 0.8139 (mt) REVERT: K 161 ASN cc_start: 0.7689 (t0) cc_final: 0.7439 (t0) REVERT: K 287 ASN cc_start: 0.8604 (t0) cc_final: 0.7974 (t0) REVERT: K 290 SER cc_start: 0.8915 (t) cc_final: 0.8514 (m) REVERT: K 329 SER cc_start: 0.8852 (m) cc_final: 0.8627 (t) REVERT: L 49 GLU cc_start: 0.7578 (pm20) cc_final: 0.7303 (mp0) REVERT: M 145 MET cc_start: 0.8588 (mmp) cc_final: 0.8215 (mmm) REVERT: N 113 MET cc_start: 0.8123 (tpt) cc_final: 0.7868 (mmm) REVERT: N 122 VAL cc_start: 0.9207 (p) cc_final: 0.8806 (m) REVERT: N 129 MET cc_start: 0.8222 (tmm) cc_final: 0.7566 (tmm) REVERT: N 132 LYS cc_start: 0.8566 (pttt) cc_final: 0.8243 (ptmt) REVERT: N 134 ASP cc_start: 0.7816 (t0) cc_final: 0.7243 (t70) REVERT: N 137 ASP cc_start: 0.8108 (p0) cc_final: 0.7845 (p0) REVERT: O 707 MET cc_start: 0.5937 (mmt) cc_final: 0.5656 (mmm) REVERT: O 746 TYR cc_start: 0.6243 (p90) cc_final: 0.5720 (p90) REVERT: P 99 PHE cc_start: 0.8771 (t80) cc_final: 0.8525 (t80) REVERT: P 123 LYS cc_start: 0.7843 (mmmt) cc_final: 0.6907 (mmtt) REVERT: P 128 VAL cc_start: 0.8474 (t) cc_final: 0.8129 (t) REVERT: P 132 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7765 (mtp85) REVERT: R 42 GLU cc_start: 0.7947 (pm20) cc_final: 0.7560 (pm20) REVERT: R 50 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7603 (mt-10) REVERT: R 56 ARG cc_start: 0.7901 (tmm160) cc_final: 0.7532 (tmm160) REVERT: R 60 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7627 (mt-10) REVERT: R 71 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7745 (t) REVERT: R 89 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7661 (mt-10) REVERT: R 101 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8290 (mmtm) REVERT: S 460 TRP cc_start: 0.8305 (m-10) cc_final: 0.7728 (m-10) REVERT: A 107 MET cc_start: 0.8142 (ttm) cc_final: 0.7913 (ttm) REVERT: A 158 LEU cc_start: 0.6951 (tp) cc_final: 0.6587 (tt) REVERT: A 1007 MET cc_start: 0.8329 (mmp) cc_final: 0.8080 (mmm) REVERT: A 1070 LYS cc_start: 0.7025 (tptt) cc_final: 0.6677 (tptt) REVERT: B 7 LEU cc_start: 0.7255 (pt) cc_final: 0.6800 (mp) REVERT: B 153 MET cc_start: 0.2673 (tmm) cc_final: 0.2422 (tmm) REVERT: B 182 CYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7481 (m) REVERT: B 183 TYR cc_start: 0.5160 (m-80) cc_final: 0.4711 (m-10) REVERT: B 611 ARG cc_start: 0.7343 (mtp180) cc_final: 0.6943 (mmm-85) REVERT: B 803 ARG cc_start: 0.6638 (ttm-80) cc_final: 0.6318 (tpp-160) REVERT: B 1170 LYS cc_start: 0.8549 (tptt) cc_final: 0.8299 (tptm) REVERT: C 39 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7916 (mppt) REVERT: C 66 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8113 (mtpp) REVERT: D 177 MET cc_start: 0.8490 (mtp) cc_final: 0.8149 (mtm) REVERT: D 263 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8064 (mtmm) REVERT: E 109 PHE cc_start: 0.7680 (m-80) cc_final: 0.7434 (m-10) REVERT: E 126 MET cc_start: 0.8558 (mmm) cc_final: 0.8191 (ppp) REVERT: E 250 CYS cc_start: 0.8414 (m) cc_final: 0.7850 (m) REVERT: E 310 MET cc_start: 0.8276 (mtm) cc_final: 0.7953 (mtp) REVERT: E 311 MET cc_start: 0.8698 (ttm) cc_final: 0.8338 (ttp) REVERT: E 831 LEU cc_start: 0.8576 (tt) cc_final: 0.8228 (pp) REVERT: E 835 GLN cc_start: 0.8481 (mt0) cc_final: 0.8126 (mp10) REVERT: F 386 LYS cc_start: 0.8503 (mttt) cc_final: 0.8077 (mmtt) REVERT: F 424 ASN cc_start: 0.6352 (m-40) cc_final: 0.6089 (t0) REVERT: F 486 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6668 (ptpp) REVERT: F 498 TYR cc_start: 0.4885 (t80) cc_final: 0.4313 (t80) REVERT: I 319 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7534 (p) REVERT: I 356 MET cc_start: 0.8205 (tpt) cc_final: 0.7875 (tpt) REVERT: J 278 MET cc_start: 0.7747 (mtm) cc_final: 0.7522 (mtp) REVERT: J 307 MET cc_start: 0.7486 (mmt) cc_final: 0.7222 (mmt) REVERT: J 346 TRP cc_start: 0.8862 (m100) cc_final: 0.8282 (m100) REVERT: J 465 MET cc_start: 0.8232 (tpt) cc_final: 0.7714 (tpt) REVERT: T 248 MET cc_start: 0.7643 (mtp) cc_final: 0.7111 (mtp) REVERT: T 431 ARG cc_start: 0.6769 (ttm-80) cc_final: 0.6002 (mtt180) REVERT: T 443 GLU cc_start: 0.6787 (tt0) cc_final: 0.5803 (tm-30) REVERT: T 445 MET cc_start: 0.6985 (ttm) cc_final: 0.6189 (mtp) outliers start: 63 outliers final: 29 residues processed: 510 average time/residue: 0.6969 time to fit residues: 574.0018 Evaluate side-chains 449 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 416 time to evaluate : 5.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 282 SER Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 259 LYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 878 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 319 VAL Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain T residue 638 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 319 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 479 optimal weight: 3.9990 chunk 392 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 576 optimal weight: 8.9990 chunk 623 optimal weight: 1.9990 chunk 513 optimal weight: 0.2980 chunk 571 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 462 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN N 87 GLN N 174 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1227 GLN D 270 GLN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 53227 Z= 0.187 Angle : 0.562 11.567 71996 Z= 0.292 Chirality : 0.043 0.237 7835 Planarity : 0.005 0.153 9296 Dihedral : 5.659 70.929 7084 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.60 % Rotamer: Outliers : 1.34 % Allowed : 7.32 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.36 (0.11), residues: 6299 helix: 0.92 (0.10), residues: 2600 sheet: -0.16 (0.18), residues: 833 loop : -0.14 (0.12), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 117 HIS 0.026 0.001 HIS D 135 PHE 0.030 0.001 PHE J 139 TYR 0.023 0.001 TYR K 200 ARG 0.018 0.000 ARG E 891 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 443 time to evaluate : 6.127 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: G 135 MET cc_start: 0.7836 (mtm) cc_final: 0.7347 (mtm) REVERT: G 204 ASP cc_start: 0.7392 (t0) cc_final: 0.6846 (t0) REVERT: K 200 TYR cc_start: 0.8450 (t80) cc_final: 0.8181 (t80) REVERT: K 287 ASN cc_start: 0.8588 (t0) cc_final: 0.8101 (t0) REVERT: K 290 SER cc_start: 0.8927 (t) cc_final: 0.8446 (m) REVERT: K 334 PHE cc_start: 0.7263 (t80) cc_final: 0.6880 (t80) REVERT: L 49 GLU cc_start: 0.7529 (pm20) cc_final: 0.7265 (mp0) REVERT: L 69 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7078 (mm) REVERT: L 194 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7992 (ptmt) REVERT: M 126 SER cc_start: 0.9102 (t) cc_final: 0.8895 (p) REVERT: M 160 PRO cc_start: 0.8685 (Cg_endo) cc_final: 0.8388 (Cg_exo) REVERT: N 113 MET cc_start: 0.7981 (tpt) cc_final: 0.7332 (tpp) REVERT: N 122 VAL cc_start: 0.9133 (p) cc_final: 0.8754 (m) REVERT: N 129 MET cc_start: 0.8139 (tmm) cc_final: 0.7493 (tmm) REVERT: N 132 LYS cc_start: 0.8567 (pttt) cc_final: 0.8229 (ptmt) REVERT: N 134 ASP cc_start: 0.7736 (t0) cc_final: 0.7270 (t70) REVERT: N 137 ASP cc_start: 0.8187 (p0) cc_final: 0.7948 (p0) REVERT: N 174 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (tp-100) REVERT: O 608 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7142 (mp0) REVERT: O 632 MET cc_start: 0.6861 (ptp) cc_final: 0.6644 (mtt) REVERT: O 707 MET cc_start: 0.6006 (mmt) cc_final: 0.5738 (mmm) REVERT: O 746 TYR cc_start: 0.6224 (p90) cc_final: 0.5698 (p90) REVERT: O 762 TRP cc_start: 0.5767 (m-10) cc_final: 0.5557 (m-10) REVERT: P 86 ILE cc_start: 0.8706 (mt) cc_final: 0.8450 (mt) REVERT: P 99 PHE cc_start: 0.8764 (t80) cc_final: 0.8513 (t80) REVERT: P 123 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7513 (tppp) REVERT: P 128 VAL cc_start: 0.8363 (t) cc_final: 0.8134 (t) REVERT: P 129 LEU cc_start: 0.8498 (mm) cc_final: 0.8200 (tp) REVERT: R 42 GLU cc_start: 0.7821 (pm20) cc_final: 0.7475 (pm20) REVERT: R 50 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7610 (mt-10) REVERT: R 56 ARG cc_start: 0.7913 (tmm160) cc_final: 0.7605 (tmm160) REVERT: R 60 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7645 (mt-10) REVERT: R 73 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8254 (tmtt) REVERT: R 101 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8306 (mmtm) REVERT: R 121 ASP cc_start: 0.7447 (m-30) cc_final: 0.7142 (m-30) REVERT: A 67 ARG cc_start: 0.7823 (tpt170) cc_final: 0.7608 (tpt170) REVERT: A 97 GLN cc_start: 0.7270 (tt0) cc_final: 0.6971 (tt0) REVERT: A 107 MET cc_start: 0.8086 (ttm) cc_final: 0.7870 (ttm) REVERT: A 158 LEU cc_start: 0.6942 (tp) cc_final: 0.6564 (tt) REVERT: A 344 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5595 (pt) REVERT: A 355 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6298 (pp) REVERT: A 633 CYS cc_start: 0.7340 (t) cc_final: 0.6788 (m) REVERT: A 841 MET cc_start: 0.8742 (mmm) cc_final: 0.8263 (mmt) REVERT: A 1070 LYS cc_start: 0.7040 (tptt) cc_final: 0.6685 (tptt) REVERT: B 7 LEU cc_start: 0.7029 (pt) cc_final: 0.6612 (mp) REVERT: B 182 CYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7422 (m) REVERT: B 183 TYR cc_start: 0.5104 (m-80) cc_final: 0.4669 (m-10) REVERT: B 410 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8557 (m) REVERT: B 611 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6954 (mmm-85) REVERT: B 803 ARG cc_start: 0.6637 (ttm-80) cc_final: 0.6278 (tpp-160) REVERT: B 1170 LYS cc_start: 0.8554 (tptt) cc_final: 0.8285 (tptm) REVERT: D 177 MET cc_start: 0.8468 (mtp) cc_final: 0.8108 (mtm) REVERT: D 263 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8090 (mtmm) REVERT: E 109 PHE cc_start: 0.7574 (m-80) cc_final: 0.7284 (m-10) REVERT: E 126 MET cc_start: 0.8556 (mmm) cc_final: 0.8162 (ppp) REVERT: E 250 CYS cc_start: 0.8165 (m) cc_final: 0.7856 (m) REVERT: E 310 MET cc_start: 0.8246 (mtm) cc_final: 0.7922 (mtp) REVERT: E 311 MET cc_start: 0.8691 (ttm) cc_final: 0.8351 (ttp) REVERT: E 405 MET cc_start: 0.7626 (mtm) cc_final: 0.7344 (mtp) REVERT: E 831 LEU cc_start: 0.8528 (tt) cc_final: 0.8186 (pp) REVERT: E 835 GLN cc_start: 0.8437 (mt0) cc_final: 0.8076 (mp10) REVERT: F 386 LYS cc_start: 0.8533 (mttt) cc_final: 0.8090 (mmtt) REVERT: F 424 ASN cc_start: 0.6248 (m-40) cc_final: 0.5975 (t0) REVERT: F 485 ASN cc_start: 0.7126 (m110) cc_final: 0.6923 (m-40) REVERT: F 486 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6679 (ptpp) REVERT: F 498 TYR cc_start: 0.4835 (t80) cc_final: 0.4115 (t80) REVERT: I 279 MET cc_start: 0.8238 (tpp) cc_final: 0.7510 (tpp) REVERT: I 356 MET cc_start: 0.8197 (tpt) cc_final: 0.7857 (tpt) REVERT: I 487 MET cc_start: 0.8191 (mmm) cc_final: 0.7916 (mmm) REVERT: J 307 MET cc_start: 0.7431 (mmt) cc_final: 0.7167 (mmt) REVERT: J 346 TRP cc_start: 0.8847 (m100) cc_final: 0.8284 (m100) REVERT: J 465 MET cc_start: 0.8297 (tpt) cc_final: 0.7713 (tpt) REVERT: T 248 MET cc_start: 0.7638 (mtp) cc_final: 0.7068 (mtp) REVERT: T 431 ARG cc_start: 0.6782 (ttm-80) cc_final: 0.5992 (mtt180) REVERT: T 443 GLU cc_start: 0.6720 (tt0) cc_final: 0.5820 (tm-30) REVERT: T 445 MET cc_start: 0.7101 (ttm) cc_final: 0.6233 (mtp) outliers start: 76 outliers final: 33 residues processed: 498 average time/residue: 0.7023 time to fit residues: 576.2930 Evaluate side-chains 454 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 414 time to evaluate : 5.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 282 SER Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain N residue 80 LYS Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 174 GLN Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 173 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 500 MET Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 856 CYS Chi-restraints excluded: chain E residue 862 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 451 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 569 optimal weight: 6.9990 chunk 433 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 275 optimal weight: 8.9990 chunk 387 optimal weight: 1.9990 chunk 578 optimal weight: 8.9990 chunk 612 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 548 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 HIS ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 HIS ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 GLN A1066 GLN B 945 ASN B 999 ASN D 81 GLN D 135 HIS F 401 HIS ** T 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 53227 Z= 0.482 Angle : 0.655 9.271 71996 Z= 0.339 Chirality : 0.048 0.265 7835 Planarity : 0.006 0.152 9296 Dihedral : 5.788 70.033 7083 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 1.71 % Allowed : 8.44 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.11), residues: 6299 helix: 0.82 (0.10), residues: 2601 sheet: -0.24 (0.17), residues: 844 loop : -0.27 (0.12), residues: 2854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 171 HIS 0.014 0.001 HIS F 346 PHE 0.033 0.002 PHE J 139 TYR 0.020 0.002 TYR K 200 ARG 0.014 0.001 ARG F 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 432 time to evaluate : 6.326 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: G 135 MET cc_start: 0.7950 (mtm) cc_final: 0.7544 (mtm) REVERT: G 144 GLN cc_start: 0.8269 (pm20) cc_final: 0.8060 (pm20) REVERT: K 169 MET cc_start: 0.7247 (mmp) cc_final: 0.6985 (mmp) REVERT: K 290 SER cc_start: 0.8943 (t) cc_final: 0.8339 (m) REVERT: L 49 GLU cc_start: 0.7526 (pm20) cc_final: 0.7247 (mp0) REVERT: L 69 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6975 (mm) REVERT: M 145 MET cc_start: 0.8668 (mmp) cc_final: 0.8352 (mmm) REVERT: M 148 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7253 (ptp-170) REVERT: M 160 PRO cc_start: 0.8764 (Cg_endo) cc_final: 0.8492 (Cg_exo) REVERT: N 98 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7913 (tt) REVERT: N 113 MET cc_start: 0.8123 (tpt) cc_final: 0.7655 (tpp) REVERT: N 122 VAL cc_start: 0.9179 (p) cc_final: 0.8821 (m) REVERT: N 129 MET cc_start: 0.8145 (tmm) cc_final: 0.7423 (tmm) REVERT: N 132 LYS cc_start: 0.8638 (pttt) cc_final: 0.8257 (ptmt) REVERT: N 134 ASP cc_start: 0.7795 (t0) cc_final: 0.7220 (t70) REVERT: N 156 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7848 (mp) REVERT: N 174 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8297 (tp-100) REVERT: O 608 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7123 (mp0) REVERT: O 746 TYR cc_start: 0.6378 (p90) cc_final: 0.5830 (p90) REVERT: P 86 ILE cc_start: 0.8744 (mt) cc_final: 0.8522 (mt) REVERT: P 123 LYS cc_start: 0.7823 (mmmt) cc_final: 0.6866 (mmtt) REVERT: P 128 VAL cc_start: 0.8384 (t) cc_final: 0.8108 (t) REVERT: P 132 ARG cc_start: 0.7948 (mmt90) cc_final: 0.7721 (mmt90) REVERT: P 135 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7406 (t0) REVERT: R 42 GLU cc_start: 0.7918 (pm20) cc_final: 0.7478 (pm20) REVERT: R 50 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7441 (mt-10) REVERT: R 56 ARG cc_start: 0.7928 (tmm160) cc_final: 0.7661 (tmm160) REVERT: R 73 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8364 (tmtt) REVERT: R 101 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8325 (mmtm) REVERT: R 121 ASP cc_start: 0.7524 (m-30) cc_final: 0.7220 (m-30) REVERT: S 314 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7403 (ttp-170) REVERT: A 97 GLN cc_start: 0.7370 (tt0) cc_final: 0.7062 (tt0) REVERT: A 107 MET cc_start: 0.7946 (ttm) cc_final: 0.7690 (ttt) REVERT: A 158 LEU cc_start: 0.6905 (tp) cc_final: 0.6508 (tt) REVERT: A 199 CYS cc_start: 0.8621 (m) cc_final: 0.8306 (m) REVERT: A 344 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5599 (pt) REVERT: A 355 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6450 (pp) REVERT: A 633 CYS cc_start: 0.7271 (t) cc_final: 0.6788 (m) REVERT: A 1007 MET cc_start: 0.8368 (mmp) cc_final: 0.8103 (mmm) REVERT: A 1064 ASN cc_start: 0.8149 (m-40) cc_final: 0.7600 (m-40) REVERT: A 1070 LYS cc_start: 0.7113 (tptt) cc_final: 0.6780 (tptt) REVERT: B 7 LEU cc_start: 0.6972 (pt) cc_final: 0.6707 (mp) REVERT: B 183 TYR cc_start: 0.5347 (m-80) cc_final: 0.4689 (m-10) REVERT: B 410 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8715 (m) REVERT: B 803 ARG cc_start: 0.6636 (ttm-80) cc_final: 0.6244 (tpp-160) REVERT: B 1170 LYS cc_start: 0.8603 (tptt) cc_final: 0.8143 (tptp) REVERT: D 115 TYR cc_start: 0.7633 (m-10) cc_final: 0.7401 (m-10) REVERT: D 177 MET cc_start: 0.8539 (mtp) cc_final: 0.8158 (mtm) REVERT: D 263 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8139 (mtmm) REVERT: E 126 MET cc_start: 0.8561 (mmm) cc_final: 0.8138 (ppp) REVERT: E 250 CYS cc_start: 0.8152 (m) cc_final: 0.7845 (m) REVERT: E 310 MET cc_start: 0.8376 (mtm) cc_final: 0.8040 (mtt) REVERT: E 311 MET cc_start: 0.8743 (ttm) cc_final: 0.8411 (ttp) REVERT: E 752 MET cc_start: 0.8184 (mtp) cc_final: 0.7895 (mtp) REVERT: F 386 LYS cc_start: 0.8496 (mttt) cc_final: 0.7966 (mmtt) REVERT: F 424 ASN cc_start: 0.6411 (m-40) cc_final: 0.6140 (t0) REVERT: F 486 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6594 (ptpp) REVERT: F 498 TYR cc_start: 0.4795 (t80) cc_final: 0.4552 (t80) REVERT: I 279 MET cc_start: 0.8212 (tpp) cc_final: 0.7546 (tpp) REVERT: J 307 MET cc_start: 0.7414 (mmt) cc_final: 0.7170 (mmt) REVERT: J 320 MET cc_start: 0.8045 (mmt) cc_final: 0.7827 (mmp) REVERT: J 325 MET cc_start: 0.8212 (ptm) cc_final: 0.7899 (ptp) REVERT: J 346 TRP cc_start: 0.8863 (m100) cc_final: 0.8296 (m100) REVERT: J 465 MET cc_start: 0.8330 (tpt) cc_final: 0.7773 (tpt) REVERT: T 248 MET cc_start: 0.7676 (mtp) cc_final: 0.6997 (mtp) REVERT: T 431 ARG cc_start: 0.6810 (ttm-80) cc_final: 0.5937 (mtt180) REVERT: T 443 GLU cc_start: 0.6761 (tt0) cc_final: 0.5754 (tm-30) REVERT: T 445 MET cc_start: 0.7205 (ttm) cc_final: 0.6288 (mtp) REVERT: T 513 MET cc_start: 0.7545 (tpp) cc_final: 0.7029 (tpp) outliers start: 97 outliers final: 58 residues processed: 506 average time/residue: 0.6731 time to fit residues: 563.4217 Evaluate side-chains 480 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 411 time to evaluate : 5.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 282 SER Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain K residue 329 SER Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 80 LYS Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 174 GLN Chi-restraints excluded: chain N residue 183 ASP Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain P residue 135 ASP Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 173 MET Chi-restraints excluded: chain S residue 259 LYS Chi-restraints excluded: chain S residue 314 ARG Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 856 CYS Chi-restraints excluded: chain E residue 862 LEU Chi-restraints excluded: chain E residue 878 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 523 ILE Chi-restraints excluded: chain J residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 510 optimal weight: 9.9990 chunk 347 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 456 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 522 optimal weight: 5.9990 chunk 423 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 550 optimal weight: 7.9990 chunk 154 optimal weight: 0.0980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN N 174 GLN P 131 ASN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN T 393 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 53227 Z= 0.258 Angle : 0.562 8.451 71996 Z= 0.293 Chirality : 0.044 0.234 7835 Planarity : 0.005 0.148 9296 Dihedral : 5.517 64.933 7083 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 1.66 % Allowed : 9.20 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.39 (0.11), residues: 6299 helix: 1.02 (0.10), residues: 2592 sheet: -0.13 (0.18), residues: 817 loop : -0.21 (0.12), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 117 HIS 0.010 0.001 HIS F 346 PHE 0.031 0.002 PHE K 166 TYR 0.016 0.001 TYR K 200 ARG 0.013 0.000 ARG A1046 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 428 time to evaluate : 6.033 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: G 135 MET cc_start: 0.7794 (mtm) cc_final: 0.7361 (mtm) REVERT: H 309 MET cc_start: 0.8803 (mmm) cc_final: 0.7853 (mmm) REVERT: K 287 ASN cc_start: 0.8721 (t0) cc_final: 0.8019 (t0) REVERT: K 290 SER cc_start: 0.8933 (t) cc_final: 0.8280 (m) REVERT: L 49 GLU cc_start: 0.7478 (pm20) cc_final: 0.7203 (mp0) REVERT: L 69 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7026 (mm) REVERT: L 91 THR cc_start: 0.6089 (OUTLIER) cc_final: 0.5882 (p) REVERT: L 184 ASP cc_start: 0.8076 (m-30) cc_final: 0.7818 (p0) REVERT: L 194 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7631 (ptmt) REVERT: M 160 PRO cc_start: 0.8745 (Cg_endo) cc_final: 0.8482 (Cg_exo) REVERT: N 122 VAL cc_start: 0.9116 (p) cc_final: 0.8762 (m) REVERT: N 129 MET cc_start: 0.8141 (tmm) cc_final: 0.7457 (tmm) REVERT: N 132 LYS cc_start: 0.8610 (pttt) cc_final: 0.8239 (ptmt) REVERT: N 134 ASP cc_start: 0.7786 (t0) cc_final: 0.7133 (t70) REVERT: N 174 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8282 (tp-100) REVERT: O 608 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7109 (mp0) REVERT: O 746 TYR cc_start: 0.6325 (p90) cc_final: 0.5739 (p90) REVERT: P 86 ILE cc_start: 0.8775 (mt) cc_final: 0.8507 (mt) REVERT: P 123 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7529 (tppp) REVERT: P 128 VAL cc_start: 0.8319 (t) cc_final: 0.7985 (t) REVERT: P 132 ARG cc_start: 0.8020 (mmt90) cc_final: 0.7805 (mmt90) REVERT: P 135 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7512 (t0) REVERT: R 42 GLU cc_start: 0.7835 (pm20) cc_final: 0.7430 (pm20) REVERT: R 50 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7479 (mt-10) REVERT: R 56 ARG cc_start: 0.8027 (tmm160) cc_final: 0.7640 (tmm160) REVERT: R 60 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7566 (mt-10) REVERT: R 101 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8313 (mmtm) REVERT: R 121 ASP cc_start: 0.7485 (m-30) cc_final: 0.7172 (m-30) REVERT: S 250 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8049 (tp) REVERT: S 314 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7319 (ttp-170) REVERT: A 97 GLN cc_start: 0.7410 (tt0) cc_final: 0.7055 (tt0) REVERT: A 158 LEU cc_start: 0.6884 (tp) cc_final: 0.6438 (tt) REVERT: A 199 CYS cc_start: 0.8573 (m) cc_final: 0.8268 (m) REVERT: A 296 MET cc_start: 0.8530 (mmm) cc_final: 0.7750 (mmm) REVERT: A 344 ILE cc_start: 0.6074 (OUTLIER) cc_final: 0.5667 (pt) REVERT: A 355 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6448 (pp) REVERT: A 633 CYS cc_start: 0.7262 (t) cc_final: 0.6756 (m) REVERT: A 1007 MET cc_start: 0.8301 (mmp) cc_final: 0.8040 (mmm) REVERT: A 1070 LYS cc_start: 0.7053 (tptt) cc_final: 0.6723 (tptt) REVERT: B 7 LEU cc_start: 0.6923 (pt) cc_final: 0.6649 (mp) REVERT: B 183 TYR cc_start: 0.5335 (m-80) cc_final: 0.4719 (m-10) REVERT: B 358 TYR cc_start: 0.7101 (m-80) cc_final: 0.6857 (m-10) REVERT: B 410 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8634 (m) REVERT: B 803 ARG cc_start: 0.6674 (ttm-80) cc_final: 0.6331 (tpp-160) REVERT: B 1170 LYS cc_start: 0.8584 (tptt) cc_final: 0.8142 (tptp) REVERT: B 1174 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7849 (ttm110) REVERT: C 39 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8176 (mppt) REVERT: D 177 MET cc_start: 0.8514 (mtp) cc_final: 0.8134 (mtm) REVERT: D 263 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8141 (mtmm) REVERT: D 279 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8084 (pp) REVERT: E 126 MET cc_start: 0.8547 (mmm) cc_final: 0.8122 (ppp) REVERT: E 250 CYS cc_start: 0.8104 (m) cc_final: 0.7803 (m) REVERT: E 310 MET cc_start: 0.8344 (mtm) cc_final: 0.8019 (mtt) REVERT: E 311 MET cc_start: 0.8733 (ttm) cc_final: 0.8415 (ttp) REVERT: E 392 ARG cc_start: 0.8748 (ttp80) cc_final: 0.8233 (ttp80) REVERT: E 511 MET cc_start: 0.8767 (mmm) cc_final: 0.8414 (ptm) REVERT: E 769 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8022 (t) REVERT: E 826 MET cc_start: 0.7655 (pmm) cc_final: 0.7445 (pmm) REVERT: E 831 LEU cc_start: 0.8618 (tp) cc_final: 0.8286 (pp) REVERT: F 386 LYS cc_start: 0.8481 (mttt) cc_final: 0.7928 (mmtt) REVERT: F 424 ASN cc_start: 0.6462 (m-40) cc_final: 0.6192 (t0) REVERT: F 486 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6607 (ptpp) REVERT: F 498 TYR cc_start: 0.4775 (t80) cc_final: 0.3990 (t80) REVERT: I 279 MET cc_start: 0.8126 (tpp) cc_final: 0.7545 (tpp) REVERT: J 307 MET cc_start: 0.7376 (mmt) cc_final: 0.7128 (mmt) REVERT: J 320 MET cc_start: 0.8090 (mmt) cc_final: 0.7682 (mmp) REVERT: J 325 MET cc_start: 0.8173 (ptm) cc_final: 0.7868 (ptp) REVERT: J 346 TRP cc_start: 0.8850 (m100) cc_final: 0.8298 (m100) REVERT: T 248 MET cc_start: 0.7632 (mtp) cc_final: 0.6951 (mtp) REVERT: T 431 ARG cc_start: 0.6785 (ttm-80) cc_final: 0.5936 (mtt180) REVERT: T 443 GLU cc_start: 0.6725 (tt0) cc_final: 0.5779 (tm-30) REVERT: T 445 MET cc_start: 0.7271 (ttm) cc_final: 0.6337 (mtp) outliers start: 94 outliers final: 57 residues processed: 506 average time/residue: 0.6800 time to fit residues: 565.0321 Evaluate side-chains 483 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 414 time to evaluate : 6.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 282 SER Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain N residue 80 LYS Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 174 GLN Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain P residue 135 ASP Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 173 MET Chi-restraints excluded: chain S residue 250 LEU Chi-restraints excluded: chain S residue 259 LYS Chi-restraints excluded: chain S residue 314 ARG Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain E residue 856 CYS Chi-restraints excluded: chain E residue 862 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 277 MET Chi-restraints excluded: chain J residue 341 THR Chi-restraints excluded: chain T residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 206 optimal weight: 0.7980 chunk 551 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 613 optimal weight: 20.0000 chunk 509 optimal weight: 0.8980 chunk 284 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS P 127 HIS P 131 ASN A 497 GLN E 226 HIS J 54 GLN T 610 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 53227 Z= 0.281 Angle : 0.557 10.869 71996 Z= 0.289 Chirality : 0.044 0.228 7835 Planarity : 0.005 0.146 9296 Dihedral : 5.403 61.154 7083 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 1.85 % Allowed : 9.71 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.48 (0.11), residues: 6299 helix: 1.13 (0.10), residues: 2588 sheet: -0.16 (0.18), residues: 832 loop : -0.18 (0.12), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 117 HIS 0.010 0.001 HIS F 346 PHE 0.028 0.002 PHE J 139 TYR 0.019 0.001 TYR E 510 ARG 0.012 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 431 time to evaluate : 6.155 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: G 135 MET cc_start: 0.7794 (mtm) cc_final: 0.7406 (mtm) REVERT: G 204 ASP cc_start: 0.8037 (m-30) cc_final: 0.7832 (m-30) REVERT: K 287 ASN cc_start: 0.8711 (t0) cc_final: 0.8012 (t0) REVERT: K 290 SER cc_start: 0.8932 (t) cc_final: 0.8318 (m) REVERT: L 49 GLU cc_start: 0.7467 (pm20) cc_final: 0.7181 (mp0) REVERT: L 69 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7033 (mm) REVERT: L 91 THR cc_start: 0.6146 (OUTLIER) cc_final: 0.5933 (p) REVERT: L 184 ASP cc_start: 0.8080 (m-30) cc_final: 0.7770 (p0) REVERT: M 160 PRO cc_start: 0.8750 (Cg_endo) cc_final: 0.8511 (Cg_exo) REVERT: N 122 VAL cc_start: 0.9102 (p) cc_final: 0.8753 (m) REVERT: N 129 MET cc_start: 0.8150 (tmm) cc_final: 0.7444 (tmm) REVERT: N 132 LYS cc_start: 0.8636 (pttt) cc_final: 0.8225 (ptmt) REVERT: N 134 ASP cc_start: 0.7763 (t0) cc_final: 0.7116 (t70) REVERT: O 608 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7105 (mp0) REVERT: O 746 TYR cc_start: 0.6383 (p90) cc_final: 0.5761 (p90) REVERT: P 86 ILE cc_start: 0.8778 (mt) cc_final: 0.8430 (mt) REVERT: P 90 LEU cc_start: 0.8501 (mt) cc_final: 0.8269 (mp) REVERT: P 123 LYS cc_start: 0.7821 (mmmt) cc_final: 0.7564 (tppp) REVERT: P 127 HIS cc_start: 0.7968 (t70) cc_final: 0.7623 (t-90) REVERT: P 128 VAL cc_start: 0.8246 (t) cc_final: 0.7763 (t) REVERT: P 135 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7520 (t0) REVERT: R 42 GLU cc_start: 0.7768 (pm20) cc_final: 0.7375 (pm20) REVERT: R 50 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7542 (mt-10) REVERT: R 56 ARG cc_start: 0.7999 (tmm160) cc_final: 0.7549 (tmm160) REVERT: R 60 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7555 (mt-10) REVERT: R 101 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8320 (mmtm) REVERT: R 121 ASP cc_start: 0.7492 (m-30) cc_final: 0.7149 (m-30) REVERT: S 250 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8052 (tp) REVERT: S 314 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7312 (ttp-170) REVERT: A 97 GLN cc_start: 0.7362 (tt0) cc_final: 0.7000 (tt0) REVERT: A 158 LEU cc_start: 0.6970 (tp) cc_final: 0.6555 (tt) REVERT: A 199 CYS cc_start: 0.8572 (m) cc_final: 0.8339 (m) REVERT: A 296 MET cc_start: 0.8606 (mmm) cc_final: 0.7803 (mmm) REVERT: A 344 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5728 (pt) REVERT: A 355 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6432 (pp) REVERT: A 633 CYS cc_start: 0.7319 (t) cc_final: 0.6818 (m) REVERT: A 901 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8684 (tp) REVERT: A 1046 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6895 (mmt-90) REVERT: A 1070 LYS cc_start: 0.7057 (tptt) cc_final: 0.6708 (tptt) REVERT: B 7 LEU cc_start: 0.6893 (pt) cc_final: 0.6604 (mp) REVERT: B 183 TYR cc_start: 0.5265 (m-80) cc_final: 0.4646 (m-10) REVERT: B 358 TYR cc_start: 0.7106 (m-80) cc_final: 0.6905 (m-10) REVERT: B 410 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8659 (m) REVERT: B 803 ARG cc_start: 0.6675 (ttm-80) cc_final: 0.6299 (tpp-160) REVERT: B 1170 LYS cc_start: 0.8544 (tptt) cc_final: 0.8238 (tptm) REVERT: D 177 MET cc_start: 0.8526 (mtp) cc_final: 0.8130 (mtm) REVERT: D 279 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8068 (pp) REVERT: E 126 MET cc_start: 0.8540 (mmm) cc_final: 0.8117 (ppp) REVERT: E 250 CYS cc_start: 0.8087 (m) cc_final: 0.7792 (m) REVERT: E 310 MET cc_start: 0.8348 (mtm) cc_final: 0.8026 (mtt) REVERT: E 311 MET cc_start: 0.8738 (ttm) cc_final: 0.8420 (ttp) REVERT: E 364 PHE cc_start: 0.8018 (m-80) cc_final: 0.7743 (m-10) REVERT: E 459 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7174 (p0) REVERT: E 511 MET cc_start: 0.8773 (mmm) cc_final: 0.8361 (ptm) REVERT: E 769 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8033 (t) REVERT: E 831 LEU cc_start: 0.8621 (tp) cc_final: 0.8305 (pp) REVERT: F 386 LYS cc_start: 0.8498 (mttt) cc_final: 0.7957 (mmtt) REVERT: F 424 ASN cc_start: 0.6424 (m-40) cc_final: 0.6161 (t0) REVERT: F 486 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6550 (ptpp) REVERT: F 498 TYR cc_start: 0.4790 (t80) cc_final: 0.3973 (t80) REVERT: I 267 MET cc_start: 0.7640 (ttm) cc_final: 0.7421 (ttp) REVERT: I 279 MET cc_start: 0.8113 (tpp) cc_final: 0.7616 (tpp) REVERT: J 307 MET cc_start: 0.7346 (mmt) cc_final: 0.7112 (mmt) REVERT: J 325 MET cc_start: 0.8197 (ptm) cc_final: 0.7909 (ptp) REVERT: J 334 MET cc_start: 0.7904 (mmm) cc_final: 0.7464 (tpp) REVERT: J 346 TRP cc_start: 0.8846 (m100) cc_final: 0.8292 (m100) REVERT: T 248 MET cc_start: 0.7637 (mtp) cc_final: 0.6963 (mtp) REVERT: T 431 ARG cc_start: 0.6706 (ttm-80) cc_final: 0.5912 (mtt180) REVERT: T 443 GLU cc_start: 0.6707 (tt0) cc_final: 0.5800 (tm-30) REVERT: T 445 MET cc_start: 0.7273 (ttm) cc_final: 0.6348 (mtp) outliers start: 105 outliers final: 68 residues processed: 514 average time/residue: 0.6812 time to fit residues: 578.9389 Evaluate side-chains 497 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 415 time to evaluate : 5.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 282 SER Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain P residue 135 ASP Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 173 MET Chi-restraints excluded: chain S residue 250 LEU Chi-restraints excluded: chain S residue 259 LYS Chi-restraints excluded: chain S residue 314 ARG Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain E residue 856 CYS Chi-restraints excluded: chain E residue 862 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 277 MET Chi-restraints excluded: chain J residue 341 THR Chi-restraints excluded: chain T residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 591 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 447 optimal weight: 0.6980 chunk 347 optimal weight: 5.9990 chunk 516 optimal weight: 6.9990 chunk 342 optimal weight: 6.9990 chunk 611 optimal weight: 10.0000 chunk 382 optimal weight: 0.9980 chunk 372 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS B 85 HIS B 244 GLN I 284 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 53227 Z= 0.445 Angle : 0.625 11.542 71996 Z= 0.323 Chirality : 0.047 0.235 7835 Planarity : 0.005 0.148 9296 Dihedral : 5.557 64.043 7082 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 2.05 % Allowed : 9.96 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.32 (0.11), residues: 6299 helix: 1.02 (0.10), residues: 2574 sheet: -0.39 (0.17), residues: 870 loop : -0.23 (0.12), residues: 2855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 117 HIS 0.010 0.001 HIS F 346 PHE 0.033 0.002 PHE J 139 TYR 0.019 0.002 TYR A 200 ARG 0.012 0.001 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 427 time to evaluate : 6.501 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: G 135 MET cc_start: 0.7937 (mtm) cc_final: 0.7585 (mtm) REVERT: G 144 GLN cc_start: 0.8448 (pm20) cc_final: 0.8203 (pm20) REVERT: G 204 ASP cc_start: 0.8039 (m-30) cc_final: 0.7826 (m-30) REVERT: H 374 MET cc_start: 0.8128 (mtm) cc_final: 0.7829 (mtm) REVERT: K 287 ASN cc_start: 0.8737 (t0) cc_final: 0.7998 (t0) REVERT: K 290 SER cc_start: 0.8978 (t) cc_final: 0.8373 (m) REVERT: L 69 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6998 (mm) REVERT: L 184 ASP cc_start: 0.8109 (m-30) cc_final: 0.7694 (p0) REVERT: M 160 PRO cc_start: 0.8802 (Cg_endo) cc_final: 0.8567 (Cg_exo) REVERT: N 122 VAL cc_start: 0.9097 (p) cc_final: 0.8757 (m) REVERT: N 132 LYS cc_start: 0.8652 (pttt) cc_final: 0.8217 (ptmt) REVERT: N 134 ASP cc_start: 0.7621 (t0) cc_final: 0.6958 (t70) REVERT: N 145 MET cc_start: 0.7796 (mmm) cc_final: 0.7575 (mmm) REVERT: N 175 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: O 608 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7136 (mp0) REVERT: O 713 MET cc_start: 0.6691 (tpp) cc_final: 0.6452 (tpp) REVERT: O 746 TYR cc_start: 0.6484 (p90) cc_final: 0.5828 (p90) REVERT: P 86 ILE cc_start: 0.8782 (mt) cc_final: 0.8554 (mt) REVERT: P 123 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7608 (tppp) REVERT: P 135 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7492 (t0) REVERT: R 42 GLU cc_start: 0.7842 (pm20) cc_final: 0.7430 (pm20) REVERT: R 50 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7422 (mt-10) REVERT: R 51 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7207 (mtp85) REVERT: R 56 ARG cc_start: 0.8070 (tmm160) cc_final: 0.7534 (tmm160) REVERT: R 60 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7587 (mt-10) REVERT: R 101 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8342 (mmtm) REVERT: R 121 ASP cc_start: 0.7498 (m-30) cc_final: 0.7146 (m-30) REVERT: S 250 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8111 (tp) REVERT: S 314 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7347 (ttp-170) REVERT: S 460 TRP cc_start: 0.8331 (m-10) cc_final: 0.7616 (m-10) REVERT: A 97 GLN cc_start: 0.7351 (tt0) cc_final: 0.7000 (tt0) REVERT: A 158 LEU cc_start: 0.6996 (tp) cc_final: 0.6584 (tt) REVERT: A 199 CYS cc_start: 0.8586 (m) cc_final: 0.8269 (m) REVERT: A 296 MET cc_start: 0.8645 (mmm) cc_final: 0.7873 (mmm) REVERT: A 344 ILE cc_start: 0.6115 (OUTLIER) cc_final: 0.5702 (pt) REVERT: A 355 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6466 (pp) REVERT: A 1070 LYS cc_start: 0.7061 (tptt) cc_final: 0.6734 (tptt) REVERT: B 7 LEU cc_start: 0.6932 (pt) cc_final: 0.6644 (mp) REVERT: B 32 MET cc_start: 0.8055 (mmt) cc_final: 0.7765 (mtt) REVERT: B 183 TYR cc_start: 0.5382 (m-80) cc_final: 0.4684 (m-10) REVERT: B 410 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8692 (m) REVERT: B 803 ARG cc_start: 0.6746 (ttm-80) cc_final: 0.6337 (tpp-160) REVERT: B 1170 LYS cc_start: 0.8538 (tptt) cc_final: 0.8229 (tptt) REVERT: D 177 MET cc_start: 0.8537 (mtp) cc_final: 0.8123 (mtm) REVERT: D 279 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8052 (pp) REVERT: E 126 MET cc_start: 0.8531 (mmm) cc_final: 0.8095 (ppp) REVERT: E 250 CYS cc_start: 0.8062 (m) cc_final: 0.7665 (m) REVERT: E 310 MET cc_start: 0.8389 (mtm) cc_final: 0.8096 (mtp) REVERT: E 311 MET cc_start: 0.8753 (ttm) cc_final: 0.8445 (ttp) REVERT: E 392 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8297 (ttp80) REVERT: E 769 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8141 (t) REVERT: F 386 LYS cc_start: 0.8457 (mttt) cc_final: 0.7870 (mmtt) REVERT: F 424 ASN cc_start: 0.6455 (m-40) cc_final: 0.6219 (t0) REVERT: F 486 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6579 (ptpp) REVERT: F 498 TYR cc_start: 0.4794 (t80) cc_final: 0.3990 (t80) REVERT: I 267 MET cc_start: 0.7704 (ttm) cc_final: 0.7499 (ttp) REVERT: I 279 MET cc_start: 0.8117 (tpp) cc_final: 0.7702 (tpp) REVERT: I 356 MET cc_start: 0.8162 (tpt) cc_final: 0.7813 (tpt) REVERT: J 284 MET cc_start: 0.8857 (tpp) cc_final: 0.8631 (mmm) REVERT: J 307 MET cc_start: 0.7367 (mmt) cc_final: 0.7131 (mmt) REVERT: J 320 MET cc_start: 0.8069 (mmt) cc_final: 0.7618 (mmp) REVERT: J 325 MET cc_start: 0.8218 (ptm) cc_final: 0.7857 (ptp) REVERT: J 346 TRP cc_start: 0.8877 (m100) cc_final: 0.8322 (m100) REVERT: T 431 ARG cc_start: 0.6690 (ttm-80) cc_final: 0.5884 (mtt180) REVERT: T 443 GLU cc_start: 0.6508 (tt0) cc_final: 0.5567 (tm-30) outliers start: 116 outliers final: 82 residues processed: 521 average time/residue: 0.7018 time to fit residues: 605.1542 Evaluate side-chains 512 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 418 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 282 SER Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 135 ASP Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 173 MET Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 250 LEU Chi-restraints excluded: chain S residue 259 LYS Chi-restraints excluded: chain S residue 314 ARG Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain S residue 380 VAL Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 872 ILE Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain E residue 856 CYS Chi-restraints excluded: chain E residue 862 LEU Chi-restraints excluded: chain E residue 878 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 375 ARG Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 523 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 277 MET Chi-restraints excluded: chain J residue 341 THR Chi-restraints excluded: chain T residue 612 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 378 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 364 optimal weight: 0.1980 chunk 184 optimal weight: 0.1980 chunk 120 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 416 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 480 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 144 GLN G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS O 671 GLN P 131 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 53227 Z= 0.172 Angle : 0.539 12.222 71996 Z= 0.278 Chirality : 0.042 0.222 7835 Planarity : 0.005 0.143 9296 Dihedral : 5.237 60.620 7082 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 1.55 % Allowed : 10.63 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.55 (0.11), residues: 6299 helix: 1.21 (0.10), residues: 2593 sheet: -0.22 (0.18), residues: 833 loop : -0.13 (0.12), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP T 117 HIS 0.005 0.001 HIS T 516 PHE 0.025 0.001 PHE J 139 TYR 0.030 0.001 TYR B 358 ARG 0.012 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 420 time to evaluate : 6.262 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: G 247 MET cc_start: 0.8083 (mmm) cc_final: 0.7620 (mmm) REVERT: H 309 MET cc_start: 0.8756 (mmm) cc_final: 0.7940 (mmm) REVERT: H 374 MET cc_start: 0.8028 (mtm) cc_final: 0.7725 (mtm) REVERT: K 287 ASN cc_start: 0.8690 (t0) cc_final: 0.8145 (t0) REVERT: K 290 SER cc_start: 0.8967 (t) cc_final: 0.8365 (m) REVERT: L 69 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7039 (mm) REVERT: L 194 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7366 (ptmt) REVERT: M 160 PRO cc_start: 0.8803 (Cg_endo) cc_final: 0.8589 (Cg_exo) REVERT: N 122 VAL cc_start: 0.9027 (p) cc_final: 0.8700 (m) REVERT: N 132 LYS cc_start: 0.8636 (pttt) cc_final: 0.8212 (ptmt) REVERT: N 134 ASP cc_start: 0.7530 (t0) cc_final: 0.6963 (t70) REVERT: N 141 PHE cc_start: 0.8580 (t80) cc_final: 0.8351 (t80) REVERT: N 145 MET cc_start: 0.7579 (mmm) cc_final: 0.7313 (mmm) REVERT: N 175 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7808 (ttp) REVERT: O 608 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7096 (mp0) REVERT: O 713 MET cc_start: 0.6842 (tpp) cc_final: 0.6640 (tpp) REVERT: O 746 TYR cc_start: 0.6412 (p90) cc_final: 0.5737 (p90) REVERT: P 82 MET cc_start: 0.6327 (tpp) cc_final: 0.6083 (tpp) REVERT: P 86 ILE cc_start: 0.8740 (mt) cc_final: 0.8452 (mt) REVERT: P 123 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7530 (tppp) REVERT: R 42 GLU cc_start: 0.7793 (pm20) cc_final: 0.7388 (pm20) REVERT: R 50 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7467 (mt-10) REVERT: R 51 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6723 (mtp85) REVERT: R 56 ARG cc_start: 0.8109 (tmm160) cc_final: 0.7566 (tmm160) REVERT: R 60 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7662 (mt-10) REVERT: R 101 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8326 (mmtm) REVERT: R 121 ASP cc_start: 0.7483 (m-30) cc_final: 0.7139 (m-30) REVERT: S 250 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7965 (tp) REVERT: S 314 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7309 (ttp-170) REVERT: A 97 GLN cc_start: 0.7327 (tt0) cc_final: 0.6955 (tt0) REVERT: A 158 LEU cc_start: 0.6998 (tp) cc_final: 0.6589 (tt) REVERT: A 199 CYS cc_start: 0.8553 (m) cc_final: 0.8340 (m) REVERT: A 296 MET cc_start: 0.8593 (mmm) cc_final: 0.7807 (mmm) REVERT: A 344 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5660 (pt) REVERT: A 355 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6360 (pp) REVERT: A 633 CYS cc_start: 0.7203 (t) cc_final: 0.6763 (m) REVERT: A 662 MET cc_start: 0.8306 (ptm) cc_final: 0.8102 (ptm) REVERT: A 841 MET cc_start: 0.8684 (mmm) cc_final: 0.8234 (mmt) REVERT: A 901 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8700 (tp) REVERT: A 1070 LYS cc_start: 0.7028 (tptt) cc_final: 0.6705 (tptt) REVERT: B 7 LEU cc_start: 0.6779 (pt) cc_final: 0.6469 (mp) REVERT: B 183 TYR cc_start: 0.5290 (m-80) cc_final: 0.4654 (m-10) REVERT: B 410 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8611 (m) REVERT: B 803 ARG cc_start: 0.6758 (ttm-80) cc_final: 0.6337 (tpp-160) REVERT: B 927 MET cc_start: 0.8551 (mtm) cc_final: 0.8136 (mtt) REVERT: B 1170 LYS cc_start: 0.8534 (tptt) cc_final: 0.8222 (tptt) REVERT: D 177 MET cc_start: 0.8466 (mtp) cc_final: 0.8147 (mtm) REVERT: E 126 MET cc_start: 0.8501 (mmm) cc_final: 0.8122 (ppp) REVERT: E 206 MET cc_start: 0.8760 (mtp) cc_final: 0.8363 (mtp) REVERT: E 250 CYS cc_start: 0.8045 (m) cc_final: 0.7785 (m) REVERT: E 310 MET cc_start: 0.8319 (mtm) cc_final: 0.8029 (mtp) REVERT: E 311 MET cc_start: 0.8727 (ttm) cc_final: 0.8398 (ttp) REVERT: E 364 PHE cc_start: 0.7776 (m-80) cc_final: 0.7550 (m-80) REVERT: E 392 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8392 (ttp80) REVERT: E 511 MET cc_start: 0.8751 (mmm) cc_final: 0.8345 (ptm) REVERT: E 769 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7869 (t) REVERT: F 386 LYS cc_start: 0.8490 (mttt) cc_final: 0.7934 (mmtt) REVERT: F 424 ASN cc_start: 0.6479 (m-40) cc_final: 0.6234 (t0) REVERT: F 486 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6575 (ptpp) REVERT: F 498 TYR cc_start: 0.4773 (t80) cc_final: 0.3962 (t80) REVERT: I 267 MET cc_start: 0.7745 (ttm) cc_final: 0.7543 (ttp) REVERT: I 279 MET cc_start: 0.8051 (tpp) cc_final: 0.7678 (tpp) REVERT: I 356 MET cc_start: 0.8172 (tpt) cc_final: 0.7932 (tpt) REVERT: J 284 MET cc_start: 0.8852 (tpp) cc_final: 0.7973 (mmm) REVERT: J 307 MET cc_start: 0.7293 (mmt) cc_final: 0.7036 (mmt) REVERT: J 325 MET cc_start: 0.8202 (ptm) cc_final: 0.7998 (ptp) REVERT: J 346 TRP cc_start: 0.8863 (m100) cc_final: 0.8317 (m100) REVERT: T 248 MET cc_start: 0.7664 (mtp) cc_final: 0.7005 (mtp) REVERT: T 431 ARG cc_start: 0.6655 (ttm-80) cc_final: 0.5857 (mtt180) REVERT: T 443 GLU cc_start: 0.6663 (tt0) cc_final: 0.5679 (tm-30) REVERT: T 463 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6528 (tp) REVERT: T 513 MET cc_start: 0.7926 (mmm) cc_final: 0.7637 (tpp) outliers start: 88 outliers final: 61 residues processed: 487 average time/residue: 0.6686 time to fit residues: 538.1991 Evaluate side-chains 479 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 406 time to evaluate : 6.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 282 SER Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain P residue 96 ARG Chi-restraints excluded: chain P residue 129 LEU Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 173 MET Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 250 LEU Chi-restraints excluded: chain S residue 314 ARG Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain E residue 856 CYS Chi-restraints excluded: chain E residue 862 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 341 THR Chi-restraints excluded: chain T residue 463 ILE Chi-restraints excluded: chain T residue 612 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 555 optimal weight: 0.0980 chunk 585 optimal weight: 5.9990 chunk 534 optimal weight: 0.1980 chunk 569 optimal weight: 7.9990 chunk 342 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 447 optimal weight: 0.8980 chunk 174 optimal weight: 0.0050 chunk 514 optimal weight: 0.5980 chunk 538 optimal weight: 0.9990 chunk 567 optimal weight: 4.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS M 182 ASN P 95 ASN S 279 ASN A 95 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 53227 Z= 0.157 Angle : 0.526 12.300 71996 Z= 0.270 Chirality : 0.042 0.225 7835 Planarity : 0.005 0.140 9296 Dihedral : 4.955 58.668 7081 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 1.41 % Allowed : 10.74 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.73 (0.11), residues: 6299 helix: 1.39 (0.10), residues: 2591 sheet: -0.06 (0.18), residues: 806 loop : -0.09 (0.12), residues: 2902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 117 HIS 0.006 0.001 HIS T 516 PHE 0.025 0.001 PHE E 830 TYR 0.027 0.001 TYR D 157 ARG 0.014 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 426 time to evaluate : 6.134 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: G 247 MET cc_start: 0.7978 (mmm) cc_final: 0.7526 (mmm) REVERT: H 309 MET cc_start: 0.8797 (mmm) cc_final: 0.8358 (mmm) REVERT: H 346 MET cc_start: 0.8712 (ttp) cc_final: 0.8272 (ttp) REVERT: H 374 MET cc_start: 0.8014 (mtm) cc_final: 0.7717 (mtm) REVERT: K 200 TYR cc_start: 0.8352 (t80) cc_final: 0.8003 (t80) REVERT: K 290 SER cc_start: 0.8967 (t) cc_final: 0.8374 (m) REVERT: L 69 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7054 (mm) REVERT: L 108 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7655 (mtp-110) REVERT: L 184 ASP cc_start: 0.8030 (m-30) cc_final: 0.7329 (p0) REVERT: L 194 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7633 (ptmt) REVERT: N 122 VAL cc_start: 0.9023 (p) cc_final: 0.8694 (m) REVERT: N 132 LYS cc_start: 0.8604 (pttt) cc_final: 0.8268 (ptpt) REVERT: N 134 ASP cc_start: 0.7329 (t0) cc_final: 0.6845 (t70) REVERT: N 175 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7791 (ttp) REVERT: O 608 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7107 (mp0) REVERT: O 713 MET cc_start: 0.6821 (tpp) cc_final: 0.6618 (tpp) REVERT: O 746 TYR cc_start: 0.6367 (p90) cc_final: 0.5688 (p90) REVERT: P 86 ILE cc_start: 0.8813 (mt) cc_final: 0.8297 (mt) REVERT: P 123 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7505 (tppp) REVERT: R 42 GLU cc_start: 0.7811 (pm20) cc_final: 0.7325 (mp0) REVERT: R 50 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7600 (mt-10) REVERT: R 56 ARG cc_start: 0.8128 (tmm160) cc_final: 0.7570 (tmm160) REVERT: R 101 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8318 (mmtm) REVERT: R 121 ASP cc_start: 0.7470 (m-30) cc_final: 0.7126 (m-30) REVERT: R 132 TYR cc_start: 0.7703 (p90) cc_final: 0.7486 (p90) REVERT: S 202 ASP cc_start: 0.7621 (t0) cc_final: 0.7264 (t0) REVERT: S 250 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7944 (tp) REVERT: A 97 GLN cc_start: 0.7417 (tt0) cc_final: 0.6861 (tt0) REVERT: A 158 LEU cc_start: 0.7028 (tp) cc_final: 0.6765 (tt) REVERT: A 296 MET cc_start: 0.8549 (mmm) cc_final: 0.8129 (mmt) REVERT: A 344 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5705 (pt) REVERT: A 355 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6384 (pp) REVERT: A 633 CYS cc_start: 0.6975 (t) cc_final: 0.6642 (m) REVERT: A 841 MET cc_start: 0.8608 (mmm) cc_final: 0.8170 (mmt) REVERT: A 901 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8661 (tp) REVERT: A 1051 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6603 (tt) REVERT: A 1070 LYS cc_start: 0.7004 (tptt) cc_final: 0.6674 (tptt) REVERT: B 7 LEU cc_start: 0.6780 (pt) cc_final: 0.6462 (mp) REVERT: B 32 MET cc_start: 0.7640 (mtt) cc_final: 0.7430 (mtt) REVERT: B 183 TYR cc_start: 0.5277 (m-80) cc_final: 0.4617 (m-10) REVERT: B 410 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8633 (m) REVERT: B 803 ARG cc_start: 0.6698 (ttm-80) cc_final: 0.6272 (tpp-160) REVERT: B 927 MET cc_start: 0.8585 (mtm) cc_final: 0.8199 (mtt) REVERT: B 1170 LYS cc_start: 0.8511 (tptt) cc_final: 0.8203 (tptt) REVERT: D 177 MET cc_start: 0.8422 (mtp) cc_final: 0.8058 (mtm) REVERT: D 279 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7925 (pp) REVERT: E 206 MET cc_start: 0.8721 (mtp) cc_final: 0.8326 (mtp) REVERT: E 250 CYS cc_start: 0.8001 (m) cc_final: 0.7754 (m) REVERT: E 310 MET cc_start: 0.8396 (mtm) cc_final: 0.8155 (mtp) REVERT: E 311 MET cc_start: 0.8735 (ttm) cc_final: 0.8395 (ttp) REVERT: E 364 PHE cc_start: 0.7603 (m-80) cc_final: 0.7387 (m-80) REVERT: E 389 ASP cc_start: 0.8231 (t70) cc_final: 0.7901 (t0) REVERT: E 392 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8435 (ttp80) REVERT: E 405 MET cc_start: 0.7492 (mtp) cc_final: 0.6789 (mtp) REVERT: E 511 MET cc_start: 0.8755 (mmm) cc_final: 0.8368 (ptm) REVERT: E 769 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7812 (t) REVERT: F 386 LYS cc_start: 0.8460 (mttt) cc_final: 0.7908 (mmtt) REVERT: F 424 ASN cc_start: 0.6474 (m-40) cc_final: 0.6050 (p0) REVERT: F 486 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6546 (ptpp) REVERT: F 498 TYR cc_start: 0.4990 (t80) cc_final: 0.4155 (t80) REVERT: I 279 MET cc_start: 0.8061 (tpp) cc_final: 0.7678 (tpp) REVERT: I 356 MET cc_start: 0.8155 (tpt) cc_final: 0.7907 (tpt) REVERT: J 284 MET cc_start: 0.8845 (tpp) cc_final: 0.8528 (mmt) REVERT: J 307 MET cc_start: 0.7307 (mmt) cc_final: 0.7037 (mmt) REVERT: J 346 TRP cc_start: 0.8865 (m100) cc_final: 0.8337 (m100) REVERT: T 248 MET cc_start: 0.7656 (mtp) cc_final: 0.7019 (mtp) REVERT: T 431 ARG cc_start: 0.6706 (ttm-80) cc_final: 0.5904 (mtt180) REVERT: T 463 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6446 (tp) outliers start: 80 outliers final: 55 residues processed: 486 average time/residue: 0.6866 time to fit residues: 553.0909 Evaluate side-chains 471 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 404 time to evaluate : 5.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain P residue 96 ARG Chi-restraints excluded: chain P residue 129 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 250 LEU Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 926 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain E residue 856 CYS Chi-restraints excluded: chain E residue 862 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 440 THR Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain J residue 341 THR Chi-restraints excluded: chain T residue 463 ILE Chi-restraints excluded: chain T residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 373 optimal weight: 0.7980 chunk 602 optimal weight: 0.0000 chunk 367 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 418 optimal weight: 4.9990 chunk 631 optimal weight: 0.7980 chunk 581 optimal weight: 5.9990 chunk 502 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 308 optimal weight: 0.0970 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS A 346 HIS A1068 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 53227 Z= 0.176 Angle : 0.536 12.598 71996 Z= 0.273 Chirality : 0.042 0.224 7835 Planarity : 0.005 0.138 9296 Dihedral : 4.914 57.641 7081 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 1.34 % Allowed : 11.00 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.79 (0.11), residues: 6299 helix: 1.44 (0.10), residues: 2582 sheet: -0.06 (0.18), residues: 824 loop : -0.03 (0.12), residues: 2893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP T 117 HIS 0.006 0.001 HIS F 346 PHE 0.023 0.001 PHE E 830 TYR 0.029 0.001 TYR K 200 ARG 0.015 0.000 ARG A 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12598 Ramachandran restraints generated. 6299 Oldfield, 0 Emsley, 6299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 404 time to evaluate : 6.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 247 MET cc_start: 0.8047 (mmm) cc_final: 0.7549 (mmm) REVERT: H 309 MET cc_start: 0.8779 (mmm) cc_final: 0.7826 (mmm) REVERT: H 346 MET cc_start: 0.8723 (ttp) cc_final: 0.8265 (ttp) REVERT: K 161 ASN cc_start: 0.7565 (t0) cc_final: 0.7332 (t0) REVERT: K 200 TYR cc_start: 0.8402 (t80) cc_final: 0.8012 (t80) REVERT: K 290 SER cc_start: 0.8903 (t) cc_final: 0.8326 (m) REVERT: L 69 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7081 (mm) REVERT: L 194 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7633 (ptmt) REVERT: N 122 VAL cc_start: 0.9000 (p) cc_final: 0.8697 (m) REVERT: N 124 TYR cc_start: 0.7004 (m-10) cc_final: 0.6771 (m-10) REVERT: N 132 LYS cc_start: 0.8605 (pttt) cc_final: 0.8270 (ptpt) REVERT: N 134 ASP cc_start: 0.7366 (t0) cc_final: 0.6874 (t70) REVERT: N 175 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7815 (ttp) REVERT: O 608 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7099 (mp0) REVERT: O 746 TYR cc_start: 0.6389 (p90) cc_final: 0.5704 (p90) REVERT: P 86 ILE cc_start: 0.8826 (mt) cc_final: 0.8489 (mt) REVERT: P 87 GLU cc_start: 0.8126 (tp30) cc_final: 0.7728 (tp30) REVERT: P 123 LYS cc_start: 0.7750 (mmmt) cc_final: 0.7495 (tppp) REVERT: R 42 GLU cc_start: 0.7800 (pm20) cc_final: 0.7298 (mp0) REVERT: R 50 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7596 (mt-10) REVERT: R 51 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6783 (mtp85) REVERT: R 60 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7449 (mt-10) REVERT: R 101 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8336 (mmtm) REVERT: R 121 ASP cc_start: 0.7474 (m-30) cc_final: 0.7121 (m-30) REVERT: S 202 ASP cc_start: 0.7701 (t0) cc_final: 0.7335 (t0) REVERT: S 250 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7928 (tp) REVERT: A 97 GLN cc_start: 0.7446 (tt0) cc_final: 0.6881 (tt0) REVERT: A 158 LEU cc_start: 0.7009 (tp) cc_final: 0.6744 (tt) REVERT: A 296 MET cc_start: 0.8537 (mmm) cc_final: 0.8102 (mmt) REVERT: A 344 ILE cc_start: 0.6180 (OUTLIER) cc_final: 0.5827 (pt) REVERT: A 355 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6447 (pp) REVERT: A 633 CYS cc_start: 0.7001 (t) cc_final: 0.6639 (m) REVERT: A 841 MET cc_start: 0.8643 (mmm) cc_final: 0.8180 (mmt) REVERT: A 901 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8619 (tp) REVERT: A 1070 LYS cc_start: 0.7006 (tptt) cc_final: 0.6676 (tptt) REVERT: B 7 LEU cc_start: 0.6784 (pt) cc_final: 0.6494 (mp) REVERT: B 183 TYR cc_start: 0.5261 (m-80) cc_final: 0.4606 (m-10) REVERT: B 410 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8636 (m) REVERT: B 803 ARG cc_start: 0.6623 (ttm-80) cc_final: 0.6230 (tpp-160) REVERT: B 927 MET cc_start: 0.8595 (mtm) cc_final: 0.8209 (mtt) REVERT: B 1170 LYS cc_start: 0.8503 (tptt) cc_final: 0.8191 (tptt) REVERT: B 1308 TRP cc_start: 0.6772 (m100) cc_final: 0.6189 (m100) REVERT: C 39 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8089 (mtmm) REVERT: D 177 MET cc_start: 0.8420 (mtp) cc_final: 0.8068 (mtm) REVERT: D 279 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7980 (pp) REVERT: E 79 MET cc_start: 0.6889 (tmm) cc_final: 0.6432 (tmm) REVERT: E 216 MET cc_start: 0.7612 (tpp) cc_final: 0.7409 (tpp) REVERT: E 250 CYS cc_start: 0.7982 (m) cc_final: 0.7738 (m) REVERT: E 310 MET cc_start: 0.8399 (mtm) cc_final: 0.8156 (mtp) REVERT: E 311 MET cc_start: 0.8737 (ttm) cc_final: 0.8403 (ttp) REVERT: E 364 PHE cc_start: 0.7609 (m-80) cc_final: 0.7398 (m-80) REVERT: E 389 ASP cc_start: 0.8231 (t70) cc_final: 0.7880 (t0) REVERT: E 392 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8431 (ttp80) REVERT: E 511 MET cc_start: 0.8740 (mmm) cc_final: 0.8293 (ptm) REVERT: E 769 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7834 (t) REVERT: F 386 LYS cc_start: 0.8457 (mttt) cc_final: 0.7909 (mmtt) REVERT: F 424 ASN cc_start: 0.6503 (m-40) cc_final: 0.6068 (p0) REVERT: F 486 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6555 (ptpp) REVERT: F 498 TYR cc_start: 0.5116 (t80) cc_final: 0.4262 (t80) REVERT: I 279 MET cc_start: 0.8103 (tpp) cc_final: 0.7686 (tpp) REVERT: I 356 MET cc_start: 0.8148 (tpt) cc_final: 0.7917 (tpt) REVERT: J 307 MET cc_start: 0.7297 (mmt) cc_final: 0.7078 (mmt) REVERT: J 346 TRP cc_start: 0.8866 (m100) cc_final: 0.8343 (m100) REVERT: T 248 MET cc_start: 0.7682 (mtp) cc_final: 0.7042 (mtp) REVERT: T 431 ARG cc_start: 0.6624 (ttm-80) cc_final: 0.5809 (mtt180) REVERT: T 463 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6510 (tp) REVERT: T 513 MET cc_start: 0.7973 (mmm) cc_final: 0.7582 (tpp) outliers start: 76 outliers final: 58 residues processed: 467 average time/residue: 0.7039 time to fit residues: 541.7797 Evaluate side-chains 469 residues out of total 5674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 399 time to evaluate : 6.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain K residue 225 SER Chi-restraints excluded: chain K residue 303 THR Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain P residue 96 ARG Chi-restraints excluded: chain P residue 129 LEU Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 MET Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 250 LEU Chi-restraints excluded: chain S residue 318 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 926 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain E residue 856 CYS Chi-restraints excluded: chain E residue 862 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain I residue 434 VAL Chi-restraints excluded: chain I residue 440 THR Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 341 THR Chi-restraints excluded: chain T residue 463 ILE Chi-restraints excluded: chain T residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 634 random chunks: chunk 399 optimal weight: 9.9990 chunk 535 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 463 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 503 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 517 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 160 ASN ** H 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 HIS T 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.083579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063467 restraints weight = 162320.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062894 restraints weight = 111855.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.063329 restraints weight = 97679.175| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 53227 Z= 0.296 Angle : 0.574 12.849 71996 Z= 0.294 Chirality : 0.044 0.224 7835 Planarity : 0.005 0.139 9296 Dihedral : 5.048 60.128 7081 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 1.53 % Allowed : 10.83 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.72 (0.11), residues: 6299 helix: 1.39 (0.10), residues: 2585 sheet: -0.13 (0.18), residues: 855 loop : -0.06 (0.12), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP T 117 HIS 0.011 0.001 HIS F 346 PHE 0.025 0.002 PHE E 830 TYR 0.030 0.001 TYR K 200 ARG 0.015 0.000 ARG A 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11245.48 seconds wall clock time: 295 minutes 3.47 seconds (17703.47 seconds total)