Starting phenix.real_space_refine on Thu Mar 21 00:23:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fni_29314/03_2024/8fni_29314.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fni_29314/03_2024/8fni_29314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fni_29314/03_2024/8fni_29314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fni_29314/03_2024/8fni_29314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fni_29314/03_2024/8fni_29314.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fni_29314/03_2024/8fni_29314.pdb" } resolution = 3.4 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= 0.001 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 187 5.16 5 C 18136 2.51 5 N 5066 2.21 5 O 5432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 GLU 68": "OE1" <-> "OE2" Residue "5 TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 122": "OE1" <-> "OE2" Residue "6 ASP 328": "OD1" <-> "OD2" Residue "6 ASP 354": "OD1" <-> "OD2" Residue "6 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 108": "OE1" <-> "OE2" Residue "7 ASP 114": "OD1" <-> "OD2" Residue "7 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 109": "OE1" <-> "OE2" Residue "8 ASP 317": "OD1" <-> "OD2" Residue "8 ASP 378": "OD1" <-> "OD2" Residue "8 ASP 446": "OD1" <-> "OD2" Residue "9 GLU 301": "OE1" <-> "OE2" Residue "9 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 357": "OD1" <-> "OD2" Residue "9 GLU 370": "OE1" <-> "OE2" Residue "9 GLU 398": "OE1" <-> "OE2" Residue "9 GLU 490": "OE1" <-> "OE2" Residue "9 ASP 498": "OD1" <-> "OD2" Residue "9 GLU 510": "OE1" <-> "OE2" Residue "9 ASP 643": "OD1" <-> "OD2" Residue "10 ASP 134": "OD1" <-> "OD2" Residue "10 GLU 135": "OE1" <-> "OE2" Residue "10 PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 GLU 523": "OE1" <-> "OE2" Residue "11 GLU 329": "OE1" <-> "OE2" Residue "11 PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "11 ASP 601": "OD1" <-> "OD2" Residue "11 TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "11 GLU 762": "OE1" <-> "OE2" Residue "13 ASP 115": "OD1" <-> "OD2" Residue "14 PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 ASP 102": "OD1" <-> "OD2" Residue "14 ASP 302": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28858 Number of models: 1 Model: "" Number of chains: 11 Chain: "m" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 453 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 16, 'rna3p': 4} Chain: "g" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 320 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 10, 'rna3p': 5} Chain: "5" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2318 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 15, 'TRANS': 280} Chain: "6" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3591 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 11, 'TRANS': 441} Chain: "7" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain breaks: 1 Chain: "8" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4056 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 24, 'TRANS': 488} Chain: "9" Number of atoms: 6662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6662 Classifications: {'peptide': 858} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "10" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3290 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 14, 'TRANS': 401} Chain breaks: 3 Chain: "11" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4918 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 34, 'TRANS': 579} Chain breaks: 3 Chain: "13" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 227 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "14" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2505 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 24, 'TRANS': 290} Time building chain proxies: 15.63, per 1000 atoms: 0.54 Number of scatterers: 28858 At special positions: 0 Unit cell: (128.502, 132.75, 204.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 187 16.00 P 37 15.00 O 5432 8.00 N 5066 7.00 C 18136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.90 Conformation dependent library (CDL) restraints added in 5.2 seconds 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6782 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 9 sheets defined 73.0% alpha, 3.4% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 9.40 Creating SS restraints... Processing helix chain '5' and resid 34 through 51 Processing helix chain '5' and resid 67 through 71 Processing helix chain '5' and resid 94 through 108 Processing helix chain '5' and resid 147 through 159 removed outlier: 3.648A pdb=" N HIS 5 151 " --> pdb=" O ASN 5 147 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 184 removed outlier: 3.924A pdb=" N TYR 5 184 " --> pdb=" O PRO 5 180 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 180 through 184' Processing helix chain '5' and resid 198 through 212 Processing helix chain '5' and resid 247 through 256 Processing helix chain '5' and resid 265 through 272 Processing helix chain '5' and resid 275 through 279 removed outlier: 3.863A pdb=" N VAL 5 279 " --> pdb=" O ARG 5 276 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 80 removed outlier: 3.767A pdb=" N GLU 6 69 " --> pdb=" O ASN 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 83 through 96 removed outlier: 3.799A pdb=" N ALA 6 96 " --> pdb=" O ARG 6 92 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 119 Processing helix chain '6' and resid 125 through 138 Processing helix chain '6' and resid 146 through 157 removed outlier: 3.686A pdb=" N VAL 6 150 " --> pdb=" O VAL 6 146 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR 6 156 " --> pdb=" O THR 6 152 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU 6 157 " --> pdb=" O ALA 6 153 " (cutoff:3.500A) Processing helix chain '6' and resid 159 through 176 Processing helix chain '6' and resid 181 through 195 removed outlier: 3.676A pdb=" N LYS 6 194 " --> pdb=" O SER 6 190 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 215 Processing helix chain '6' and resid 220 through 234 Processing helix chain '6' and resid 238 through 252 Processing helix chain '6' and resid 257 through 272 Proline residue: 6 263 - end of helix removed outlier: 3.927A pdb=" N GLY 6 272 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) Processing helix chain '6' and resid 276 through 289 removed outlier: 3.928A pdb=" N LYS 6 280 " --> pdb=" O PRO 6 276 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG 6 281 " --> pdb=" O LYS 6 277 " (cutoff:3.500A) Processing helix chain '6' and resid 290 through 293 Processing helix chain '6' and resid 294 through 309 Processing helix chain '6' and resid 313 through 326 Processing helix chain '6' and resid 331 through 346 Processing helix chain '6' and resid 349 through 363 Processing helix chain '6' and resid 368 through 383 Processing helix chain '6' and resid 387 through 400 removed outlier: 3.541A pdb=" N SER 6 399 " --> pdb=" O SER 6 395 " (cutoff:3.500A) Processing helix chain '6' and resid 401 through 404 removed outlier: 3.799A pdb=" N PHE 6 404 " --> pdb=" O ALA 6 401 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 401 through 404' Processing helix chain '6' and resid 405 through 419 removed outlier: 4.013A pdb=" N VAL 6 410 " --> pdb=" O ALA 6 406 " (cutoff:3.500A) Processing helix chain '6' and resid 423 through 434 Processing helix chain '6' and resid 437 through 441 removed outlier: 3.664A pdb=" N LEU 6 441 " --> pdb=" O CYS 6 438 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 457 Processing helix chain '6' and resid 460 through 474 Proline residue: 6 466 - end of helix Processing helix chain '6' and resid 474 through 480 Processing helix chain '6' and resid 484 through 496 Processing helix chain '6' and resid 500 through 508 Processing helix chain '7' and resid 81 through 97 removed outlier: 3.905A pdb=" N THR 7 97 " --> pdb=" O ARG 7 93 " (cutoff:3.500A) Processing helix chain '7' and resid 112 through 118 removed outlier: 4.023A pdb=" N LEU 7 118 " --> pdb=" O ASP 7 114 " (cutoff:3.500A) Processing helix chain '7' and resid 119 through 125 Processing helix chain '7' and resid 127 through 145 Processing helix chain '8' and resid 22 through 33 Processing helix chain '8' and resid 39 through 53 Processing helix chain '8' and resid 61 through 74 removed outlier: 3.650A pdb=" N MET 8 65 " --> pdb=" O ASP 8 61 " (cutoff:3.500A) Processing helix chain '8' and resid 76 through 80 removed outlier: 3.862A pdb=" N VAL 8 79 " --> pdb=" O ASP 8 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE 8 80 " --> pdb=" O GLN 8 77 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 76 through 80' Processing helix chain '8' and resid 81 through 96 removed outlier: 3.779A pdb=" N VAL 8 95 " --> pdb=" O THR 8 91 " (cutoff:3.500A) Processing helix chain '8' and resid 113 through 127 removed outlier: 3.828A pdb=" N ILE 8 118 " --> pdb=" O PRO 8 114 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU 8 119 " --> pdb=" O GLU 8 115 " (cutoff:3.500A) Processing helix chain '8' and resid 131 through 141 Processing helix chain '8' and resid 145 through 149 removed outlier: 3.745A pdb=" N PHE 8 149 " --> pdb=" O LEU 8 146 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 164 removed outlier: 3.630A pdb=" N SER 8 155 " --> pdb=" O PRO 8 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR 8 159 " --> pdb=" O SER 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 182 removed outlier: 3.950A pdb=" N VAL 8 172 " --> pdb=" O ASN 8 168 " (cutoff:3.500A) Processing helix chain '8' and resid 183 through 186 Processing helix chain '8' and resid 187 through 201 Processing helix chain '8' and resid 205 through 219 removed outlier: 3.726A pdb=" N LEU 8 209 " --> pdb=" O SER 8 205 " (cutoff:3.500A) Processing helix chain '8' and resid 220 through 223 removed outlier: 3.719A pdb=" N PHE 8 223 " --> pdb=" O MET 8 220 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 220 through 223' Processing helix chain '8' and resid 224 through 239 Processing helix chain '8' and resid 242 through 254 removed outlier: 3.648A pdb=" N PHE 8 246 " --> pdb=" O PHE 8 242 " (cutoff:3.500A) Processing helix chain '8' and resid 261 through 276 Processing helix chain '8' and resid 279 through 293 removed outlier: 4.070A pdb=" N ILE 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP 8 284 " --> pdb=" O ARG 8 280 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE 8 285 " --> pdb=" O GLU 8 281 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL 8 293 " --> pdb=" O ALA 8 289 " (cutoff:3.500A) Processing helix chain '8' and resid 294 through 297 removed outlier: 3.566A pdb=" N LEU 8 297 " --> pdb=" O ALA 8 294 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 294 through 297' Processing helix chain '8' and resid 298 through 312 Processing helix chain '8' and resid 316 through 332 removed outlier: 3.625A pdb=" N PHE 8 320 " --> pdb=" O SER 8 316 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY 8 321 " --> pdb=" O ASP 8 317 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG 8 329 " --> pdb=" O SER 8 325 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR 8 330 " --> pdb=" O CYS 8 326 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA 8 332 " --> pdb=" O ILE 8 328 " (cutoff:3.500A) Processing helix chain '8' and resid 333 through 334 No H-bonds generated for 'chain '8' and resid 333 through 334' Processing helix chain '8' and resid 335 through 338 Processing helix chain '8' and resid 339 through 349 Processing helix chain '8' and resid 353 through 368 Processing helix chain '8' and resid 372 through 383 Processing helix chain '8' and resid 386 through 390 Processing helix chain '8' and resid 393 through 406 removed outlier: 4.000A pdb=" N LEU 8 397 " --> pdb=" O PRO 8 393 " (cutoff:3.500A) Processing helix chain '8' and resid 410 through 424 removed outlier: 3.769A pdb=" N ALA 8 415 " --> pdb=" O PRO 8 411 " (cutoff:3.500A) Processing helix chain '8' and resid 428 through 443 Processing helix chain '8' and resid 446 through 449 Processing helix chain '8' and resid 450 through 461 removed outlier: 3.848A pdb=" N THR 8 460 " --> pdb=" O GLY 8 456 " (cutoff:3.500A) Processing helix chain '8' and resid 464 through 479 Proline residue: 8 477 - end of helix Processing helix chain '8' and resid 480 through 482 No H-bonds generated for 'chain '8' and resid 480 through 482' Processing helix chain '8' and resid 483 through 498 Processing helix chain '8' and resid 501 through 516 removed outlier: 4.091A pdb=" N TYR 8 505 " --> pdb=" O ASP 8 501 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN 8 514 " --> pdb=" O SER 8 510 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE 8 515 " --> pdb=" O ARG 8 511 " (cutoff:3.500A) Processing helix chain '8' and resid 524 through 533 Processing helix chain '9' and resid 2 through 13 Processing helix chain '9' and resid 20 through 35 Processing helix chain '9' and resid 36 through 38 No H-bonds generated for 'chain '9' and resid 36 through 38' Processing helix chain '9' and resid 39 through 41 No H-bonds generated for 'chain '9' and resid 39 through 41' Processing helix chain '9' and resid 42 through 57 Proline residue: 9 49 - end of helix Processing helix chain '9' and resid 59 through 68 removed outlier: 4.238A pdb=" N SER 9 63 " --> pdb=" O ASP 9 59 " (cutoff:3.500A) Processing helix chain '9' and resid 76 through 88 removed outlier: 4.293A pdb=" N ARG 9 80 " --> pdb=" O THR 9 76 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU 9 84 " --> pdb=" O ARG 9 80 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU 9 85 " --> pdb=" O ALA 9 81 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG 9 86 " --> pdb=" O ALA 9 82 " (cutoff:3.500A) Processing helix chain '9' and resid 94 through 112 removed outlier: 3.635A pdb=" N TRP 9 98 " --> pdb=" O ASP 9 94 " (cutoff:3.500A) Processing helix chain '9' and resid 115 through 130 removed outlier: 3.930A pdb=" N HIS 9 125 " --> pdb=" O VAL 9 121 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG 9 128 " --> pdb=" O ALA 9 124 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY 9 129 " --> pdb=" O HIS 9 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY 9 130 " --> pdb=" O ALA 9 126 " (cutoff:3.500A) Processing helix chain '9' and resid 134 through 147 removed outlier: 4.418A pdb=" N ALA 9 138 " --> pdb=" O PRO 9 134 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER 9 145 " --> pdb=" O GLU 9 141 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER 9 147 " --> pdb=" O PHE 9 143 " (cutoff:3.500A) Processing helix chain '9' and resid 155 through 164 removed outlier: 3.742A pdb=" N ILE 9 162 " --> pdb=" O ALA 9 158 " (cutoff:3.500A) Processing helix chain '9' and resid 166 through 171 removed outlier: 4.158A pdb=" N ARG 9 171 " --> pdb=" O GLU 9 168 " (cutoff:3.500A) Processing helix chain '9' and resid 172 through 185 removed outlier: 4.198A pdb=" N GLN 9 176 " --> pdb=" O SER 9 172 " (cutoff:3.500A) Processing helix chain '9' and resid 190 through 202 removed outlier: 3.868A pdb=" N GLY 9 195 " --> pdb=" O PRO 9 191 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN 9 196 " --> pdb=" O ALA 9 192 " (cutoff:3.500A) Processing helix chain '9' and resid 208 through 218 removed outlier: 4.005A pdb=" N GLU 9 218 " --> pdb=" O ALA 9 214 " (cutoff:3.500A) Processing helix chain '9' and resid 218 through 223 Processing helix chain '9' and resid 227 through 241 removed outlier: 3.552A pdb=" N GLN 9 241 " --> pdb=" O PHE 9 237 " (cutoff:3.500A) Processing helix chain '9' and resid 250 through 259 removed outlier: 4.127A pdb=" N LEU 9 254 " --> pdb=" O ALA 9 250 " (cutoff:3.500A) Processing helix chain '9' and resid 265 through 278 Processing helix chain '9' and resid 280 through 282 No H-bonds generated for 'chain '9' and resid 280 through 282' Processing helix chain '9' and resid 283 through 308 removed outlier: 5.967A pdb=" N ARG 9 289 " --> pdb=" O PRO 9 285 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU 9 290 " --> pdb=" O GLU 9 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE 9 297 " --> pdb=" O GLU 9 293 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 9 300 " --> pdb=" O GLU 9 296 " (cutoff:3.500A) Processing helix chain '9' and resid 309 through 313 Processing helix chain '9' and resid 320 through 337 removed outlier: 3.703A pdb=" N SER 9 326 " --> pdb=" O GLY 9 322 " (cutoff:3.500A) Processing helix chain '9' and resid 347 through 362 removed outlier: 3.811A pdb=" N ALA 9 351 " --> pdb=" O THR 9 347 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG 9 362 " --> pdb=" O TYR 9 358 " (cutoff:3.500A) Processing helix chain '9' and resid 363 through 369 Processing helix chain '9' and resid 375 through 382 removed outlier: 4.190A pdb=" N HIS 9 379 " --> pdb=" O SER 9 375 " (cutoff:3.500A) Processing helix chain '9' and resid 385 through 403 Processing helix chain '9' and resid 407 through 422 Processing helix chain '9' and resid 426 through 439 Processing helix chain '9' and resid 444 through 458 Processing helix chain '9' and resid 469 through 499 removed outlier: 3.686A pdb=" N ASP 9 480 " --> pdb=" O LEU 9 476 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN 9 491 " --> pdb=" O PHE 9 487 " (cutoff:3.500A) Processing helix chain '9' and resid 501 through 516 Processing helix chain '9' and resid 521 through 533 Processing helix chain '9' and resid 543 through 554 Processing helix chain '9' and resid 555 through 562 Processing helix chain '9' and resid 562 through 575 removed outlier: 3.571A pdb=" N HIS 9 566 " --> pdb=" O HIS 9 562 " (cutoff:3.500A) Processing helix chain '9' and resid 584 through 593 Processing helix chain '9' and resid 602 through 618 Processing helix chain '9' and resid 622 through 635 removed outlier: 3.537A pdb=" N LEU 9 626 " --> pdb=" O ASP 9 622 " (cutoff:3.500A) Processing helix chain '9' and resid 636 through 640 Processing helix chain '9' and resid 644 through 655 removed outlier: 3.510A pdb=" N GLY 9 650 " --> pdb=" O LYS 9 646 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE 9 652 " --> pdb=" O PHE 9 648 " (cutoff:3.500A) Processing helix chain '9' and resid 659 through 673 removed outlier: 3.652A pdb=" N LEU 9 663 " --> pdb=" O GLN 9 659 " (cutoff:3.500A) Processing helix chain '9' and resid 680 through 693 Processing helix chain '9' and resid 698 through 709 removed outlier: 3.894A pdb=" N VAL 9 702 " --> pdb=" O TYR 9 698 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE 9 709 " --> pdb=" O PHE 9 705 " (cutoff:3.500A) Processing helix chain '9' and resid 710 through 716 removed outlier: 3.598A pdb=" N TRP 9 714 " --> pdb=" O SER 9 710 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU 9 716 " --> pdb=" O GLU 9 712 " (cutoff:3.500A) Processing helix chain '9' and resid 718 through 732 Processing helix chain '9' and resid 736 through 751 removed outlier: 3.864A pdb=" N VAL 9 741 " --> pdb=" O PRO 9 737 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS 9 742 " --> pdb=" O GLN 9 738 " (cutoff:3.500A) Processing helix chain '9' and resid 752 through 754 No H-bonds generated for 'chain '9' and resid 752 through 754' Processing helix chain '9' and resid 755 through 769 Processing helix chain '9' and resid 774 through 787 Processing helix chain '9' and resid 788 through 791 Processing helix chain '9' and resid 792 through 801 Processing helix chain '9' and resid 804 through 809 removed outlier: 3.956A pdb=" N LEU 9 808 " --> pdb=" O GLY 9 804 " (cutoff:3.500A) Processing helix chain '9' and resid 811 through 826 Proline residue: 9 817 - end of helix Processing helix chain '9' and resid 828 through 842 Processing helix chain '9' and resid 845 through 857 Processing helix chain '10' and resid 117 through 141 removed outlier: 4.150A pdb=" N ALA10 121 " --> pdb=" O THR10 117 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL10 125 " --> pdb=" O ALA10 121 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU10 126 " --> pdb=" O HIS10 122 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA10 137 " --> pdb=" O ALA10 133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS10 141 " --> pdb=" O ALA10 137 " (cutoff:3.500A) Processing helix chain '10' and resid 155 through 183 Processing helix chain '10' and resid 184 through 189 removed outlier: 3.791A pdb=" N ARG10 188 " --> pdb=" O PRO10 184 " (cutoff:3.500A) Processing helix chain '10' and resid 191 through 207 removed outlier: 3.834A pdb=" N LYS10 205 " --> pdb=" O THR10 201 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU10 206 " --> pdb=" O THR10 202 " (cutoff:3.500A) Processing helix chain '10' and resid 211 through 233 removed outlier: 3.585A pdb=" N MET10 221 " --> pdb=" O ALA10 217 " (cutoff:3.500A) Processing helix chain '10' and resid 236 through 249 removed outlier: 3.988A pdb=" N LEU10 241 " --> pdb=" O ALA10 237 " (cutoff:3.500A) Processing helix chain '10' and resid 254 through 265 Processing helix chain '10' and resid 275 through 289 removed outlier: 3.854A pdb=" N THR10 289 " --> pdb=" O ARG10 285 " (cutoff:3.500A) Processing helix chain '10' and resid 294 through 296 No H-bonds generated for 'chain '10' and resid 294 through 296' Processing helix chain '10' and resid 297 through 308 removed outlier: 3.663A pdb=" N MET10 308 " --> pdb=" O VAL10 304 " (cutoff:3.500A) Processing helix chain '10' and resid 308 through 315 Processing helix chain '10' and resid 320 through 334 removed outlier: 3.505A pdb=" N HIS10 334 " --> pdb=" O CYS10 330 " (cutoff:3.500A) Processing helix chain '10' and resid 338 through 340 No H-bonds generated for 'chain '10' and resid 338 through 340' Processing helix chain '10' and resid 341 through 350 removed outlier: 3.513A pdb=" N ALA10 345 " --> pdb=" O LEU10 341 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA10 348 " --> pdb=" O LEU10 344 " (cutoff:3.500A) Processing helix chain '10' and resid 356 through 370 removed outlier: 4.064A pdb=" N ALA10 361 " --> pdb=" O PRO10 357 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR10 362 " --> pdb=" O HIS10 358 " (cutoff:3.500A) Processing helix chain '10' and resid 374 through 387 removed outlier: 3.646A pdb=" N ARG10 380 " --> pdb=" O GLU10 376 " (cutoff:3.500A) Processing helix chain '10' and resid 392 through 408 Processing helix chain '10' and resid 416 through 418 No H-bonds generated for 'chain '10' and resid 416 through 418' Processing helix chain '10' and resid 419 through 436 removed outlier: 3.681A pdb=" N THR10 423 " --> pdb=" O ASN10 419 " (cutoff:3.500A) Processing helix chain '10' and resid 445 through 459 removed outlier: 3.843A pdb=" N ILE10 449 " --> pdb=" O ALA10 445 " (cutoff:3.500A) Processing helix chain '10' and resid 464 through 483 removed outlier: 4.238A pdb=" N ILE10 481 " --> pdb=" O ASP10 477 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL10 482 " --> pdb=" O MET10 478 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET10 483 " --> pdb=" O VAL10 479 " (cutoff:3.500A) Processing helix chain '10' and resid 502 through 517 Processing helix chain '10' and resid 521 through 535 removed outlier: 3.687A pdb=" N GLN10 526 " --> pdb=" O PRO10 522 " (cutoff:3.500A) Processing helix chain '11' and resid 194 through 207 Processing helix chain '11' and resid 208 through 213 removed outlier: 6.207A pdb=" N ARG11 211 " --> pdb=" O LYS11 208 " (cutoff:3.500A) Processing helix chain '11' and resid 214 through 229 Proline residue: 11 223 - end of helix Processing helix chain '11' and resid 230 through 232 No H-bonds generated for 'chain '11' and resid 230 through 232' Processing helix chain '11' and resid 233 through 243 removed outlier: 3.719A pdb=" N CYS11 243 " --> pdb=" O ASP11 239 " (cutoff:3.500A) Processing helix chain '11' and resid 246 through 253 Processing helix chain '11' and resid 253 through 277 Processing helix chain '11' and resid 326 through 331 Processing helix chain '11' and resid 332 through 345 removed outlier: 3.835A pdb=" N MET11 345 " --> pdb=" O ILE11 341 " (cutoff:3.500A) Processing helix chain '11' and resid 350 through 367 Processing helix chain '11' and resid 368 through 371 Processing helix chain '11' and resid 373 through 388 removed outlier: 3.889A pdb=" N LEU11 377 " --> pdb=" O ASP11 373 " (cutoff:3.500A) Processing helix chain '11' and resid 392 through 407 Processing helix chain '11' and resid 413 through 427 Processing helix chain '11' and resid 431 through 464 removed outlier: 4.227A pdb=" N PHE11 435 " --> pdb=" O GLN11 431 " (cutoff:3.500A) Processing helix chain '11' and resid 524 through 541 Processing helix chain '11' and resid 543 through 557 Processing helix chain '11' and resid 565 through 570 removed outlier: 4.560A pdb=" N VAL11 570 " --> pdb=" O ARG11 566 " (cutoff:3.500A) Processing helix chain '11' and resid 572 through 577 Processing helix chain '11' and resid 581 through 596 Processing helix chain '11' and resid 599 through 613 Proline residue: 11 605 - end of helix Processing helix chain '11' and resid 620 through 632 Processing helix chain '11' and resid 641 through 656 removed outlier: 3.521A pdb=" N LEU11 645 " --> pdb=" O ASN11 641 " (cutoff:3.500A) Processing helix chain '11' and resid 686 through 701 removed outlier: 3.730A pdb=" N LYS11 701 " --> pdb=" O LYS11 697 " (cutoff:3.500A) Processing helix chain '11' and resid 705 through 729 Proline residue: 11 711 - end of helix removed outlier: 3.511A pdb=" N LYS11 728 " --> pdb=" O TYR11 724 " (cutoff:3.500A) Processing helix chain '11' and resid 733 through 748 removed outlier: 3.557A pdb=" N VAL11 737 " --> pdb=" O SER11 733 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN11 748 " --> pdb=" O CYS11 744 " (cutoff:3.500A) Processing helix chain '11' and resid 754 through 769 Processing helix chain '11' and resid 770 through 777 removed outlier: 3.938A pdb=" N GLU11 774 " --> pdb=" O GLU11 770 " (cutoff:3.500A) Processing helix chain '11' and resid 780 through 795 Processing helix chain '11' and resid 806 through 819 Processing helix chain '11' and resid 821 through 836 Processing helix chain '11' and resid 841 through 858 removed outlier: 4.136A pdb=" N GLY11 858 " --> pdb=" O ALA11 854 " (cutoff:3.500A) Processing helix chain '11' and resid 881 through 895 Processing helix chain '11' and resid 897 through 902 Processing helix chain '11' and resid 903 through 918 removed outlier: 3.567A pdb=" N TRP11 907 " --> pdb=" O SER11 903 " (cutoff:3.500A) Processing helix chain '11' and resid 920 through 934 Processing helix chain '13' and resid 116 through 121 removed outlier: 3.816A pdb=" N ARG13 119 " --> pdb=" O ALA13 116 " (cutoff:3.500A) Processing helix chain '13' and resid 123 through 128 Processing helix chain '14' and resid 39 through 43 removed outlier: 3.655A pdb=" N ARG14 43 " --> pdb=" O LYS14 40 " (cutoff:3.500A) Processing helix chain '14' and resid 49 through 53 Processing helix chain '14' and resid 70 through 74 removed outlier: 3.686A pdb=" N PHE14 73 " --> pdb=" O PHE14 70 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL14 74 " --> pdb=" O GLY14 71 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 70 through 74' Processing helix chain '14' and resid 76 through 87 Processing helix chain '14' and resid 97 through 112 Processing helix chain '14' and resid 120 through 124 Processing helix chain '14' and resid 143 through 146 Processing helix chain '14' and resid 149 through 155 removed outlier: 3.609A pdb=" N ILE14 154 " --> pdb=" O MET14 150 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR14 155 " --> pdb=" O HIS14 151 " (cutoff:3.500A) Processing helix chain '14' and resid 156 through 167 removed outlier: 3.894A pdb=" N ALA14 162 " --> pdb=" O THR14 158 " (cutoff:3.500A) Processing helix chain '14' and resid 194 through 198 removed outlier: 3.530A pdb=" N ARG14 198 " --> pdb=" O ASN14 195 " (cutoff:3.500A) Processing helix chain '14' and resid 229 through 237 removed outlier: 3.510A pdb=" N ARG14 232 " --> pdb=" O GLY14 229 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP14 233 " --> pdb=" O SER14 230 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ARG14 234 " --> pdb=" O HIS14 231 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU14 235 " --> pdb=" O ARG14 232 " (cutoff:3.500A) Processing helix chain '14' and resid 249 through 261 removed outlier: 4.076A pdb=" N GLN14 253 " --> pdb=" O ASP14 249 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE14 257 " --> pdb=" O GLN14 253 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TRP14 258 " --> pdb=" O LEU14 254 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU14 259 " --> pdb=" O ASN14 255 " (cutoff:3.500A) Processing helix chain '14' and resid 262 through 272 removed outlier: 3.770A pdb=" N ASP14 271 " --> pdb=" O GLU14 267 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR14 272 " --> pdb=" O MET14 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '5' and resid 12 through 16 removed outlier: 6.410A pdb=" N ALA 5 13 " --> pdb=" O HIS 5 59 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET 5 61 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL 5 15 " --> pdb=" O MET 5 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '5' and resid 76 through 79 Processing sheet with id=AA3, first strand: chain '5' and resid 132 through 134 removed outlier: 3.569A pdb=" N ILE 5 138 " --> pdb=" O ASP 5 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '5' and resid 185 through 188 removed outlier: 6.300A pdb=" N LEU 5 193 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU 5 222 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR 5 195 " --> pdb=" O LEU 5 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 228 through 230 Processing sheet with id=AA6, first strand: chain '11' and resid 861 through 864 Processing sheet with id=AA7, first strand: chain '14' and resid 88 through 90 removed outlier: 3.810A pdb=" N VAL14 304 " --> pdb=" O LYS14 182 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR14 176 " --> pdb=" O HIS14 310 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N MET14 312 " --> pdb=" O LEU14 174 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU14 174 " --> pdb=" O MET14 312 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA14 126 " --> pdb=" O GLN14 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '14' and resid 88 through 90 removed outlier: 3.810A pdb=" N VAL14 304 " --> pdb=" O LYS14 182 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR14 176 " --> pdb=" O HIS14 310 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N MET14 312 " --> pdb=" O LEU14 174 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU14 174 " --> pdb=" O MET14 312 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL14 172 " --> pdb=" O PHE14 346 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE14 346 " --> pdb=" O VAL14 172 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU14 174 " --> pdb=" O VAL14 344 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL14 344 " --> pdb=" O LEU14 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '14' and resid 190 through 193 removed outlier: 5.161A pdb=" N THR14 295 " --> pdb=" O PRO14 191 " (cutoff:3.500A) 1703 hydrogen bonds defined for protein. 4989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 9.73 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8915 1.34 - 1.46: 4576 1.46 - 1.58: 15607 1.58 - 1.70: 72 1.70 - 1.82: 311 Bond restraints: 29481 Sorted by residual: bond pdb=" N THR14 121 " pdb=" CA THR14 121 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.98e+00 bond pdb=" CB PRO 6 350 " pdb=" CG PRO 6 350 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.22e+00 bond pdb=" CA ARG13 131 " pdb=" CB ARG13 131 " ideal model delta sigma weight residual 1.531 1.574 -0.043 3.28e-02 9.30e+02 1.76e+00 bond pdb=" C3' U g -2 " pdb=" O3' U g -2 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.55e+00 bond pdb=" CB GLN 9 240 " pdb=" CG GLN 9 240 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 29476 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.40: 757 105.40 - 112.55: 15425 112.55 - 119.70: 9881 119.70 - 126.85: 13604 126.85 - 134.00: 409 Bond angle restraints: 40076 Sorted by residual: angle pdb=" CB MET14 270 " pdb=" CG MET14 270 " pdb=" SD MET14 270 " ideal model delta sigma weight residual 112.70 123.69 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C3' U g -2 " pdb=" O3' U g -2 " pdb=" P U g -1 " ideal model delta sigma weight residual 120.20 125.61 -5.41 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C3' A m 120 " pdb=" O3' A m 120 " pdb=" P G m 121 " ideal model delta sigma weight residual 120.20 125.12 -4.92 1.50e+00 4.44e-01 1.07e+01 angle pdb=" CA GLN 9 240 " pdb=" CB GLN 9 240 " pdb=" CG GLN 9 240 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CA MET 9 295 " pdb=" CB MET 9 295 " pdb=" CG MET 9 295 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.01e+01 ... (remaining 40071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 17483 33.26 - 66.53: 526 66.53 - 99.79: 37 99.79 - 133.05: 0 133.05 - 166.32: 3 Dihedral angle restraints: 18049 sinusoidal: 7634 harmonic: 10415 Sorted by residual: dihedral pdb=" O4' U g -16 " pdb=" C1' U g -16 " pdb=" N1 U g -16 " pdb=" C2 U g -16 " ideal model delta sinusoidal sigma weight residual 200.00 44.15 155.85 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U g -10 " pdb=" C1' U g -10 " pdb=" N1 U g -10 " pdb=" C2 U g -10 " ideal model delta sinusoidal sigma weight residual -160.00 -69.11 -90.89 1 1.50e+01 4.44e-03 4.33e+01 dihedral pdb=" O4' A m 117 " pdb=" C1' A m 117 " pdb=" N9 A m 117 " pdb=" C4 A m 117 " ideal model delta sinusoidal sigma weight residual 68.00 153.37 -85.37 1 1.70e+01 3.46e-03 3.05e+01 ... (remaining 18046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3619 0.043 - 0.086: 820 0.086 - 0.128: 165 0.128 - 0.171: 8 0.171 - 0.214: 4 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CB VAL 6 376 " pdb=" CA VAL 6 376 " pdb=" CG1 VAL 6 376 " pdb=" CG2 VAL 6 376 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' U g -2 " pdb=" C4' U g -2 " pdb=" O3' U g -2 " pdb=" C2' U g -2 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" C3' A m 120 " pdb=" C4' A m 120 " pdb=" O3' A m 120 " pdb=" C2' A m 120 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 4613 not shown) Planarity restraints: 5048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN 6 349 " 0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO 6 350 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO 6 350 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 6 350 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 9 344 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO 9 345 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO 9 345 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO 9 345 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U m 105 " 0.022 2.00e-02 2.50e+03 1.20e-02 3.22e+00 pdb=" N1 U m 105 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U m 105 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U m 105 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U m 105 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U m 105 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U m 105 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U m 105 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U m 105 " -0.003 2.00e-02 2.50e+03 ... (remaining 5045 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5767 2.78 - 3.31: 28569 3.31 - 3.84: 47055 3.84 - 4.37: 54099 4.37 - 4.90: 93593 Nonbonded interactions: 229083 Sorted by model distance: nonbonded pdb=" OG SER11 214 " pdb=" OD1 ASP11 216 " model vdw 2.247 2.440 nonbonded pdb=" OE2 GLU 9 398 " pdb=" NE2 GLN 9 402 " model vdw 2.249 2.520 nonbonded pdb=" O ALA 9 151 " pdb=" NE ARG 9 181 " model vdw 2.256 2.520 nonbonded pdb=" OP1 A m 119 " pdb=" NH2 ARG 6 370 " model vdw 2.264 2.520 nonbonded pdb=" O GLU 9 364 " pdb=" OG SER 9 368 " model vdw 2.265 2.440 ... (remaining 229078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.250 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 81.900 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.002 0.074 29481 Z= 0.143 Angle : 0.496 10.992 40076 Z= 0.260 Chirality : 0.037 0.214 4616 Planarity : 0.004 0.072 5048 Dihedral : 15.360 166.318 11267 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.03 % Allowed : 8.82 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.15), residues: 3527 helix: 1.75 (0.11), residues: 2341 sheet: 0.37 (0.47), residues: 112 loop : -0.69 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 9 114 HIS 0.013 0.001 HIS 9 342 PHE 0.015 0.001 PHE10 161 TYR 0.020 0.001 TYR 5 232 ARG 0.008 0.000 ARG11 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 9 26 MET cc_start: -0.1713 (ttp) cc_final: -0.2609 (mmm) REVERT: 9 106 LEU cc_start: 0.5450 (tt) cc_final: 0.4898 (tp) REVERT: 9 647 TYR cc_start: 0.8414 (m-80) cc_final: 0.8027 (m-80) REVERT: 13 129 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7662 (ptm160) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.3922 time to fit residues: 151.9304 Evaluate side-chains 215 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 11 residue 360 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 171 GLN ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 236 ASN ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 29481 Z= 0.432 Angle : 0.621 7.756 40076 Z= 0.320 Chirality : 0.043 0.216 4616 Planarity : 0.005 0.058 5048 Dihedral : 10.297 166.090 4431 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.74 % Allowed : 11.08 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.14), residues: 3527 helix: 1.65 (0.11), residues: 2358 sheet: 0.15 (0.46), residues: 113 loop : -0.90 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 7 145 HIS 0.011 0.001 HIS11 749 PHE 0.022 0.002 PHE 9 649 TYR 0.015 0.002 TYR10 200 ARG 0.007 0.001 ARG 6 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 209 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 306 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: 8 523 MET cc_start: 0.8135 (ptt) cc_final: 0.7915 (ptm) REVERT: 9 398 GLU cc_start: 0.6864 (tp30) cc_final: 0.6599 (tp30) outliers start: 53 outliers final: 28 residues processed: 249 average time/residue: 0.3871 time to fit residues: 160.4466 Evaluate side-chains 227 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 6 residue 437 VAL Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 8 residue 185 ASP Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 656 VAL Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 11 residue 592 MET Chi-restraints excluded: chain 11 residue 630 LEU Chi-restraints excluded: chain 11 residue 694 VAL Chi-restraints excluded: chain 11 residue 737 VAL Chi-restraints excluded: chain 11 residue 919 MET Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 287 optimal weight: 0.4980 chunk 320 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29481 Z= 0.171 Angle : 0.473 7.543 40076 Z= 0.244 Chirality : 0.037 0.203 4616 Planarity : 0.004 0.055 5048 Dihedral : 10.053 165.898 4428 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.64 % Allowed : 11.70 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.14), residues: 3527 helix: 1.90 (0.11), residues: 2373 sheet: 0.25 (0.47), residues: 108 loop : -0.78 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP14 199 HIS 0.009 0.001 HIS 9 342 PHE 0.012 0.001 PHE 9 649 TYR 0.011 0.001 TYR14 176 ARG 0.005 0.000 ARG11 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 291 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9069 (t) REVERT: 8 306 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8395 (m-80) REVERT: 9 106 LEU cc_start: 0.5594 (tt) cc_final: 0.5051 (tp) REVERT: 9 470 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5685 (mp0) REVERT: 14 102 ASP cc_start: 0.8003 (m-30) cc_final: 0.7764 (m-30) outliers start: 50 outliers final: 25 residues processed: 269 average time/residue: 0.3720 time to fit residues: 164.9462 Evaluate side-chains 231 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 249 ASP Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 319 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 216 optimal weight: 20.0000 chunk 324 optimal weight: 4.9990 chunk 343 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 307 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 423 GLN ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 153 GLN ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 254 ASN 11 429 HIS 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 29481 Z= 0.474 Angle : 0.639 7.998 40076 Z= 0.327 Chirality : 0.043 0.232 4616 Planarity : 0.005 0.056 5048 Dihedral : 10.190 165.728 4428 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.75 % Allowed : 13.18 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.14), residues: 3527 helix: 1.60 (0.11), residues: 2354 sheet: -0.11 (0.43), residues: 126 loop : -0.93 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 7 145 HIS 0.016 0.002 HIS 9 342 PHE 0.029 0.002 PHE 9 649 TYR 0.016 0.002 TYR10 200 ARG 0.007 0.001 ARG 6 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 211 time to evaluate : 3.303 Fit side-chains revert: symmetry clash REVERT: 5 210 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: 8 306 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: 9 106 LEU cc_start: 0.5956 (tt) cc_final: 0.5467 (tp) REVERT: 9 398 GLU cc_start: 0.6761 (tp30) cc_final: 0.6520 (tp30) REVERT: 9 481 MET cc_start: 0.7362 (tpp) cc_final: 0.7130 (tpp) REVERT: 9 510 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: 14 49 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8543 (t0) REVERT: 14 102 ASP cc_start: 0.8088 (m-30) cc_final: 0.7792 (m-30) REVERT: 14 201 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7685 (m90) REVERT: 14 257 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8230 (tp) outliers start: 84 outliers final: 52 residues processed: 279 average time/residue: 0.3530 time to fit residues: 165.5245 Evaluate side-chains 258 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 200 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 437 VAL Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 7 residue 109 LEU Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 185 ASP Chi-restraints excluded: chain 8 residue 243 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 460 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 319 VAL Chi-restraints excluded: chain 9 residue 334 LEU Chi-restraints excluded: chain 9 residue 342 HIS Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 510 GLU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 656 VAL Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 723 VAL Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 11 residue 592 MET Chi-restraints excluded: chain 11 residue 630 LEU Chi-restraints excluded: chain 11 residue 737 VAL Chi-restraints excluded: chain 11 residue 919 MET Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 150 MET Chi-restraints excluded: chain 14 residue 201 HIS Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 243 SER Chi-restraints excluded: chain 14 residue 257 ILE Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 141 optimal weight: 40.0000 chunk 292 optimal weight: 20.0000 chunk 237 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 307 optimal weight: 30.0000 chunk 86 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 423 GLN ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29481 Z= 0.223 Angle : 0.509 7.985 40076 Z= 0.261 Chirality : 0.038 0.208 4616 Planarity : 0.004 0.054 5048 Dihedral : 10.030 165.821 4428 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.16 % Allowed : 14.26 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.14), residues: 3527 helix: 1.80 (0.11), residues: 2360 sheet: -0.19 (0.44), residues: 121 loop : -0.79 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 199 HIS 0.015 0.001 HIS 9 342 PHE 0.017 0.001 PHE 9 649 TYR 0.013 0.001 TYR 8 51 ARG 0.005 0.000 ARG11 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 213 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 210 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: 5 217 MET cc_start: 0.7664 (mtm) cc_final: 0.7392 (mtm) REVERT: 8 306 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: 9 106 LEU cc_start: 0.5898 (tt) cc_final: 0.5334 (tp) REVERT: 9 315 LEU cc_start: 0.7710 (mp) cc_final: 0.7509 (mt) REVERT: 9 398 GLU cc_start: 0.6589 (tp30) cc_final: 0.6287 (tp30) REVERT: 9 510 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: 11 260 MET cc_start: 0.6331 (tmm) cc_final: 0.5973 (ttp) REVERT: 14 49 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8384 (t0) REVERT: 14 102 ASP cc_start: 0.7997 (m-30) cc_final: 0.7742 (m-30) outliers start: 66 outliers final: 42 residues processed: 267 average time/residue: 0.3587 time to fit residues: 161.6576 Evaluate side-chains 248 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 229 ASN Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 7 residue 127 GLU Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 317 ASP Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 211 MET Chi-restraints excluded: chain 9 residue 249 ASP Chi-restraints excluded: chain 9 residue 334 LEU Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 510 GLU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 656 VAL Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 140 CYS Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 243 SER Chi-restraints excluded: chain 14 residue 259 GLU Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 115 optimal weight: 0.9990 chunk 309 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 699 GLN 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29481 Z= 0.186 Angle : 0.489 8.521 40076 Z= 0.249 Chirality : 0.038 0.206 4616 Planarity : 0.004 0.053 5048 Dihedral : 9.908 165.511 4428 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.30 % Allowed : 14.49 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.14), residues: 3527 helix: 1.95 (0.11), residues: 2368 sheet: -0.12 (0.44), residues: 122 loop : -0.73 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP11 245 HIS 0.014 0.001 HIS 9 342 PHE 0.014 0.001 PHE 9 649 TYR 0.011 0.001 TYR14 196 ARG 0.007 0.000 ARG11 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 214 time to evaluate : 3.308 Fit side-chains revert: symmetry clash REVERT: 5 210 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: 5 217 MET cc_start: 0.7707 (mtm) cc_final: 0.7408 (mtm) REVERT: 8 306 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: 9 398 GLU cc_start: 0.6682 (tp30) cc_final: 0.5863 (tp30) REVERT: 9 402 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: 9 510 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: 14 49 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8323 (t0) REVERT: 14 102 ASP cc_start: 0.8000 (m-30) cc_final: 0.7722 (m-30) REVERT: 14 150 MET cc_start: 0.8673 (mmp) cc_final: 0.8383 (mtp) outliers start: 70 outliers final: 51 residues processed: 274 average time/residue: 0.3508 time to fit residues: 162.6463 Evaluate side-chains 262 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 6 residue 66 ILE Chi-restraints excluded: chain 6 residue 124 ASP Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 229 ASN Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 185 ASP Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 317 ASP Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 211 MET Chi-restraints excluded: chain 9 residue 249 ASP Chi-restraints excluded: chain 9 residue 319 VAL Chi-restraints excluded: chain 9 residue 334 LEU Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 510 GLU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 711 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 630 LEU Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 331 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 289 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 119 GLN ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29481 Z= 0.272 Angle : 0.523 8.226 40076 Z= 0.266 Chirality : 0.039 0.216 4616 Planarity : 0.004 0.052 5048 Dihedral : 9.929 165.670 4428 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.72 % Allowed : 14.52 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.14), residues: 3527 helix: 1.92 (0.11), residues: 2360 sheet: -0.15 (0.42), residues: 127 loop : -0.76 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP11 245 HIS 0.012 0.001 HIS 9 342 PHE 0.018 0.001 PHE 9 649 TYR 0.014 0.001 TYR 8 51 ARG 0.005 0.000 ARG11 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 213 time to evaluate : 3.289 Fit side-chains revert: symmetry clash REVERT: 5 210 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: 5 217 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7444 (mtm) REVERT: 6 254 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: 8 306 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: 9 106 LEU cc_start: 0.5788 (tt) cc_final: 0.5120 (tp) REVERT: 9 398 GLU cc_start: 0.6724 (tp30) cc_final: 0.6059 (tp30) REVERT: 9 402 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: 9 510 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: 14 49 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8404 (t0) REVERT: 14 102 ASP cc_start: 0.7996 (m-30) cc_final: 0.7695 (m-30) REVERT: 14 325 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8806 (mt) outliers start: 83 outliers final: 68 residues processed: 284 average time/residue: 0.3580 time to fit residues: 172.1924 Evaluate side-chains 283 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 207 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 119 GLN Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 217 MET Chi-restraints excluded: chain 6 residue 66 ILE Chi-restraints excluded: chain 6 residue 124 ASP Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 229 ASN Chi-restraints excluded: chain 6 residue 254 GLU Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 7 residue 118 LEU Chi-restraints excluded: chain 7 residue 127 GLU Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 185 ASP Chi-restraints excluded: chain 8 residue 243 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 317 ASP Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 460 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 211 MET Chi-restraints excluded: chain 9 residue 249 ASP Chi-restraints excluded: chain 9 residue 268 THR Chi-restraints excluded: chain 9 residue 319 VAL Chi-restraints excluded: chain 9 residue 334 LEU Chi-restraints excluded: chain 9 residue 342 HIS Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 510 GLU Chi-restraints excluded: chain 9 residue 551 CYS Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 656 VAL Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 711 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 321 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 454 LYS Chi-restraints excluded: chain 11 residue 630 LEU Chi-restraints excluded: chain 11 residue 737 VAL Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 140 CYS Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 259 GLU Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Chi-restraints excluded: chain 14 residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 211 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 233 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 119 GLN ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29481 Z= 0.184 Angle : 0.487 9.394 40076 Z= 0.248 Chirality : 0.037 0.205 4616 Planarity : 0.004 0.052 5048 Dihedral : 9.858 165.668 4428 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.39 % Allowed : 15.02 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.14), residues: 3527 helix: 2.01 (0.11), residues: 2368 sheet: -0.11 (0.44), residues: 122 loop : -0.73 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP11 245 HIS 0.013 0.001 HIS 9 342 PHE 0.013 0.001 PHE 9 649 TYR 0.010 0.001 TYR14 176 ARG 0.007 0.000 ARG11 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 217 time to evaluate : 2.726 Fit side-chains revert: symmetry clash REVERT: 5 210 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: 5 217 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7426 (mtm) REVERT: 8 306 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: 9 106 LEU cc_start: 0.5823 (tt) cc_final: 0.5173 (tp) REVERT: 9 142 GLU cc_start: 0.6728 (tp30) cc_final: 0.6436 (tp30) REVERT: 9 398 GLU cc_start: 0.6693 (tp30) cc_final: 0.5995 (tp30) REVERT: 9 402 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: 14 49 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8305 (t0) REVERT: 14 102 ASP cc_start: 0.7984 (m-30) cc_final: 0.7695 (m-30) REVERT: 14 325 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8784 (mt) outliers start: 73 outliers final: 57 residues processed: 277 average time/residue: 0.3835 time to fit residues: 179.4056 Evaluate side-chains 273 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 5 residue 217 MET Chi-restraints excluded: chain 6 residue 66 ILE Chi-restraints excluded: chain 6 residue 124 ASP Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 229 ASN Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 7 residue 127 GLU Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 185 ASP Chi-restraints excluded: chain 8 residue 243 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 317 ASP Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 211 MET Chi-restraints excluded: chain 9 residue 249 ASP Chi-restraints excluded: chain 9 residue 268 THR Chi-restraints excluded: chain 9 residue 319 VAL Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 551 CYS Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 711 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 512 LEU Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 140 CYS Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 259 GLU Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Chi-restraints excluded: chain 14 residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 311 optimal weight: 40.0000 chunk 327 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 138 optimal weight: 0.2980 chunk 250 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 288 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 317 optimal weight: 8.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 485 GLN 11 928 ASN 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 29481 Z= 0.361 Angle : 0.577 9.614 40076 Z= 0.293 Chirality : 0.041 0.212 4616 Planarity : 0.004 0.051 5048 Dihedral : 10.000 165.257 4428 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.62 % Allowed : 15.15 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.14), residues: 3527 helix: 1.81 (0.11), residues: 2361 sheet: -0.20 (0.42), residues: 127 loop : -0.82 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP11 245 HIS 0.012 0.001 HIS 9 342 PHE 0.022 0.002 PHE 9 649 TYR 0.018 0.002 TYR 5 232 ARG 0.004 0.000 ARG 6 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 210 time to evaluate : 3.382 Fit side-chains revert: symmetry clash REVERT: 5 210 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7091 (mp10) REVERT: 8 306 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: 9 106 LEU cc_start: 0.5801 (tt) cc_final: 0.5234 (tp) REVERT: 9 142 GLU cc_start: 0.6667 (tp30) cc_final: 0.6313 (tp30) REVERT: 9 398 GLU cc_start: 0.6790 (tp30) cc_final: 0.6205 (tp30) REVERT: 9 402 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6742 (mp10) REVERT: 14 49 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8388 (t0) REVERT: 14 102 ASP cc_start: 0.8041 (m-30) cc_final: 0.7754 (m-30) REVERT: 14 325 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8815 (mt) outliers start: 80 outliers final: 67 residues processed: 279 average time/residue: 0.3611 time to fit residues: 169.9944 Evaluate side-chains 279 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 207 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 6 residue 66 ILE Chi-restraints excluded: chain 6 residue 124 ASP Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 229 ASN Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 437 VAL Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 7 residue 109 LEU Chi-restraints excluded: chain 7 residue 118 LEU Chi-restraints excluded: chain 7 residue 127 GLU Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 185 ASP Chi-restraints excluded: chain 8 residue 243 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 317 ASP Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 475 ILE Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 211 MET Chi-restraints excluded: chain 9 residue 249 ASP Chi-restraints excluded: chain 9 residue 319 VAL Chi-restraints excluded: chain 9 residue 334 LEU Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 551 CYS Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 656 VAL Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 711 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 269 SER Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 11 residue 737 VAL Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 140 CYS Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 259 GLU Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Chi-restraints excluded: chain 14 residue 316 THR Chi-restraints excluded: chain 14 residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 209 optimal weight: 1.9990 chunk 337 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 chunk 353 optimal weight: 0.9990 chunk 325 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 928 ASN 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29481 Z= 0.158 Angle : 0.487 8.676 40076 Z= 0.248 Chirality : 0.037 0.203 4616 Planarity : 0.004 0.052 5048 Dihedral : 9.842 165.324 4428 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.64 % Allowed : 16.30 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.14), residues: 3527 helix: 2.02 (0.11), residues: 2368 sheet: -0.14 (0.44), residues: 122 loop : -0.71 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP14 175 HIS 0.015 0.001 HIS 9 342 PHE 0.010 0.001 PHE 6 242 TYR 0.018 0.001 TYR 5 232 ARG 0.006 0.000 ARG11 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 214 time to evaluate : 3.177 Fit side-chains revert: symmetry clash REVERT: 5 210 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: 5 217 MET cc_start: 0.7465 (mtm) cc_final: 0.7255 (mtm) REVERT: 8 306 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: 9 106 LEU cc_start: 0.5687 (tt) cc_final: 0.5139 (tp) REVERT: 9 142 GLU cc_start: 0.6509 (tp30) cc_final: 0.6246 (tp30) REVERT: 9 398 GLU cc_start: 0.6655 (tp30) cc_final: 0.6048 (tp30) REVERT: 9 402 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6556 (mp10) REVERT: 11 723 MET cc_start: 0.5985 (mmp) cc_final: 0.5231 (ttm) REVERT: 14 49 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8266 (t0) REVERT: 14 102 ASP cc_start: 0.7962 (m-30) cc_final: 0.7684 (m-30) outliers start: 50 outliers final: 44 residues processed: 256 average time/residue: 0.3598 time to fit residues: 154.9185 Evaluate side-chains 258 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 210 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 168 ASP Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 210 GLN Chi-restraints excluded: chain 6 residue 66 ILE Chi-restraints excluded: chain 6 residue 124 ASP Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 137 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 243 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 211 MET Chi-restraints excluded: chain 9 residue 249 ASP Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 551 CYS Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 140 CYS Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Chi-restraints excluded: chain 14 residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 223 optimal weight: 8.9990 chunk 300 optimal weight: 8.9990 chunk 86 optimal weight: 0.0170 chunk 259 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 282 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 ASN ** 14 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106397 restraints weight = 51943.353| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.26 r_work: 0.3111 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29481 Z= 0.243 Angle : 0.524 11.791 40076 Z= 0.265 Chirality : 0.039 0.245 4616 Planarity : 0.004 0.052 5048 Dihedral : 9.854 165.112 4428 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 16.10 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.14), residues: 3527 helix: 1.97 (0.11), residues: 2369 sheet: -0.18 (0.43), residues: 122 loop : -0.78 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP11 245 HIS 0.015 0.001 HIS 9 342 PHE 0.016 0.001 PHE 9 649 TYR 0.018 0.001 TYR 5 232 ARG 0.006 0.000 ARG11 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5463.00 seconds wall clock time: 99 minutes 48.20 seconds (5988.20 seconds total)