Starting phenix.real_space_refine on Sat Feb 17 01:05:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/02_2024/8fnc_29308.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/02_2024/8fnc_29308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/02_2024/8fnc_29308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/02_2024/8fnc_29308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/02_2024/8fnc_29308.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnc_29308/02_2024/8fnc_29308.pdb" } resolution = 3.3 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= 0.000 sd= 0.006 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 33 5.49 5 S 116 5.16 5 C 10655 2.51 5 N 2969 2.21 5 O 3244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 ASP 56": "OD1" <-> "OD2" Residue "5 GLU 68": "OE1" <-> "OE2" Residue "5 GLU 85": "OE1" <-> "OE2" Residue "5 ASP 163": "OD1" <-> "OD2" Residue "5 ASP 206": "OD1" <-> "OD2" Residue "5 TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 181": "OD1" <-> "OD2" Residue "6 TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 291": "OD1" <-> "OD2" Residue "6 GLU 329": "OE1" <-> "OE2" Residue "6 PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 351": "OE1" <-> "OE2" Residue "6 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 110": "OD1" <-> "OD2" Residue "7 GLU 120": "OE1" <-> "OE2" Residue "7 GLU 146": "OE1" <-> "OE2" Residue "8 ASP 61": "OD1" <-> "OD2" Residue "8 ASP 63": "OD1" <-> "OD2" Residue "8 ASP 76": "OD1" <-> "OD2" Residue "8 GLU 115": "OE1" <-> "OE2" Residue "8 ASP 131": "OD1" <-> "OD2" Residue "8 ASP 170": "OD1" <-> "OD2" Residue "8 GLU 181": "OE1" <-> "OE2" Residue "8 ASP 185": "OD1" <-> "OD2" Residue "8 GLU 281": "OE1" <-> "OE2" Residue "8 TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 354": "OD1" <-> "OD2" Residue "8 GLU 366": "OE1" <-> "OE2" Residue "8 GLU 391": "OE1" <-> "OE2" Residue "8 ASP 407": "OD1" <-> "OD2" Residue "8 GLU 430": "OE1" <-> "OE2" Residue "8 GLU 437": "OE1" <-> "OE2" Residue "8 GLU 486": "OE1" <-> "OE2" Residue "10 GLU 128": "OE1" <-> "OE2" Residue "10 GLU 135": "OE1" <-> "OE2" Residue "10 PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 GLU 164": "OE1" <-> "OE2" Residue "10 GLU 193": "OE1" <-> "OE2" Residue "10 ASP 208": "OD1" <-> "OD2" Residue "10 GLU 211": "OE1" <-> "OE2" Residue "10 ASP 239": "OD1" <-> "OD2" Residue "10 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 GLU 272": "OE1" <-> "OE2" Residue "10 ASP 275": "OD1" <-> "OD2" Residue "10 ASP 318": "OD1" <-> "OD2" Residue "10 GLU 376": "OE1" <-> "OE2" Residue "10 GLU 421": "OE1" <-> "OE2" Residue "10 ASP 439": "OD1" <-> "OD2" Residue "10 GLU 442": "OE1" <-> "OE2" Residue "10 ASP 454": "OD1" <-> "OD2" Residue "10 ASP 487": "OD1" <-> "OD2" Residue "10 ASP 488": "OD1" <-> "OD2" Residue "10 PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 GLU 540": "OE1" <-> "OE2" Residue "14 GLU 48": "OE1" <-> "OE2" Residue "14 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 ASP 78": "OD1" <-> "OD2" Residue "14 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 GLU 107": "OE1" <-> "OE2" Residue "14 GLU 110": "OE1" <-> "OE2" Residue "14 ASP 215": "OD1" <-> "OD2" Residue "14 GLU 235": "OE1" <-> "OE2" Residue "14 ASP 249": "OD1" <-> "OD2" Residue "14 GLU 263": "OE1" <-> "OE2" Residue "14 ASP 278": "OD1" <-> "OD2" Residue "14 ASP 302": "OD1" <-> "OD2" Residue "14 ASP 334": "OD1" <-> "OD2" Residue "14 ASP 347": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17017 Number of models: 1 Model: "" Number of chains: 8 Chain: "m" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 369 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 3} Chain: "g" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 8, 'rna3p': 7} Chain: "5" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2327 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain: "6" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3582 Classifications: {'peptide': 452} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 440} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 547 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "8" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4076 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 25, 'TRANS': 490} 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: "14" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2496 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 24, 'TRANS': 289} Time building chain proxies: 9.39, per 1000 atoms: 0.55 Number of scatterers: 17017 At special positions: 0 Unit cell: (112.572, 130.626, 136.998, 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 116 16.00 P 33 15.00 O 3244 8.00 N 2969 7.00 C 10655 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: 7.37 Conformation dependent library (CDL) restraints added in 3.1 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 67.2% alpha, 5.8% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain '5' and resid 27 through 31 removed outlier: 3.638A pdb=" N ILE 5 31 " --> pdb=" O PRO 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 52 Processing helix chain '5' and resid 66 through 74 removed outlier: 4.126A pdb=" N VAL 5 72 " --> pdb=" O ALA 5 69 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA 5 73 " --> pdb=" O LEU 5 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP 5 74 " --> pdb=" O ARG 5 71 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 93 No H-bonds generated for 'chain '5' and resid 91 through 93' Processing helix chain '5' and resid 94 through 108 removed outlier: 3.862A pdb=" N TYR 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 121 removed outlier: 3.666A pdb=" N THR 5 121 " --> pdb=" O TYR 5 117 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 159 Processing helix chain '5' and resid 180 through 183 Processing helix chain '5' and resid 198 through 212 Processing helix chain '5' and resid 246 through 256 removed outlier: 3.735A pdb=" N MET 5 250 " --> pdb=" O TYR 5 246 " (cutoff:3.500A) Processing helix chain '5' and resid 265 through 271 Processing helix chain '6' and resid 62 through 79 Processing helix chain '6' and resid 83 through 95 Processing helix chain '6' and resid 105 through 119 removed outlier: 3.504A pdb=" N PHE 6 119 " --> pdb=" O THR 6 115 " (cutoff:3.500A) Processing helix chain '6' and resid 125 through 138 Processing helix chain '6' and resid 146 through 157 removed outlier: 4.529A pdb=" N THR 6 156 " --> pdb=" O THR 6 152 " (cutoff:3.500A) removed outlier: 4.243A 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: 3.769A pdb=" N THR 6 186 " --> pdb=" O ALA 6 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 216 removed outlier: 3.987A pdb=" N VAL 6 216 " --> pdb=" O THR 6 212 " (cutoff:3.500A) Processing helix chain '6' and resid 220 through 234 Processing helix chain '6' and resid 238 through 253 Processing helix chain '6' and resid 254 through 256 No H-bonds generated for 'chain '6' and resid 254 through 256' Processing helix chain '6' and resid 257 through 272 Proline residue: 6 263 - end of helix removed outlier: 3.815A pdb=" N GLY 6 272 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) Processing helix chain '6' and resid 275 through 288 removed outlier: 3.751A pdb=" N SER 6 279 " --> pdb=" O ASP 6 275 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS 6 280 " --> pdb=" O PRO 6 276 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG 6 281 " --> pdb=" O LYS 6 277 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU 6 288 " --> pdb=" O THR 6 284 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 309 removed outlier: 3.692A pdb=" N GLY 6 309 " --> pdb=" O PHE 6 305 " (cutoff:3.500A) Processing helix chain '6' and resid 312 through 326 removed outlier: 4.066A pdb=" N VAL 6 318 " --> pdb=" O GLN 6 314 " (cutoff:3.500A) Processing helix chain '6' and resid 331 through 346 Processing helix chain '6' and resid 349 through 361 removed outlier: 3.796A pdb=" N ASN 6 355 " --> pdb=" O GLU 6 351 " (cutoff:3.500A) Processing helix chain '6' and resid 363 through 367 Processing helix chain '6' and resid 368 through 382 Processing helix chain '6' and resid 386 through 400 Processing helix chain '6' and resid 401 through 404 removed outlier: 3.534A 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: 3.772A pdb=" N VAL 6 410 " --> pdb=" O ALA 6 406 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR 6 419 " --> pdb=" O ALA 6 415 " (cutoff:3.500A) Processing helix chain '6' and resid 423 through 434 removed outlier: 3.544A pdb=" N ALA 6 429 " --> pdb=" O ASP 6 425 " (cutoff:3.500A) Processing helix chain '6' and resid 435 through 441 removed outlier: 3.659A pdb=" N CYS 6 438 " --> pdb=" O VAL 6 435 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ARG 6 439 " --> pdb=" O TYR 6 436 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 456 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 481 through 483 No H-bonds generated for 'chain '6' and resid 481 through 483' Processing helix chain '6' and resid 484 through 496 removed outlier: 3.639A pdb=" N ASP 6 493 " --> pdb=" O GLU 6 489 " (cutoff:3.500A) Processing helix chain '6' and resid 500 through 509 Processing helix chain '7' and resid 81 through 98 Processing helix chain '7' and resid 103 through 117 Processing helix chain '7' and resid 119 through 124 Processing helix chain '7' and resid 127 through 145 removed outlier: 3.757A pdb=" N LYS 7 143 " --> pdb=" O ALA 7 139 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR 7 144 " --> pdb=" O TYR 7 140 " (cutoff:3.500A) Processing helix chain '8' and resid 21 through 33 Processing helix chain '8' and resid 39 through 53 Processing helix chain '8' and resid 61 through 74 removed outlier: 3.645A pdb=" N GLY 8 67 " --> pdb=" O ASP 8 63 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 96 removed outlier: 3.684A pdb=" N VAL 8 95 " --> pdb=" O THR 8 91 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 112 removed outlier: 3.782A pdb=" N ILE 8 112 " --> pdb=" O GLU 8 109 " (cutoff:3.500A) Processing helix chain '8' and resid 113 through 127 removed outlier: 3.685A pdb=" N LEU 8 121 " --> pdb=" O LEU 8 117 " (cutoff:3.500A) Processing helix chain '8' and resid 131 through 143 Processing helix chain '8' and resid 145 through 149 removed outlier: 3.622A pdb=" N PHE 8 149 " --> pdb=" O LEU 8 146 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 164 removed outlier: 3.575A pdb=" N SER 8 155 " --> pdb=" O PRO 8 151 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 182 removed outlier: 3.748A pdb=" N TYR 8 182 " --> pdb=" O ARG 8 178 " (cutoff:3.500A) Processing helix chain '8' and resid 187 through 201 Processing helix chain '8' and resid 205 through 218 Processing helix chain '8' and resid 224 through 239 Processing helix chain '8' and resid 242 through 253 Processing helix chain '8' and resid 261 through 276 Processing helix chain '8' and resid 279 through 294 removed outlier: 3.694A pdb=" N ILE 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU 8 292 " --> pdb=" O ASP 8 288 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL 8 293 " --> pdb=" O ALA 8 289 " (cutoff:3.500A) Processing helix chain '8' and resid 295 through 297 No H-bonds generated for 'chain '8' and resid 295 through 297' Processing helix chain '8' and resid 298 through 312 Processing helix chain '8' and resid 316 through 332 removed outlier: 4.145A pdb=" N ARG 8 329 " --> pdb=" O SER 8 325 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR 8 330 " --> pdb=" O CYS 8 326 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA 8 332 " --> pdb=" O ILE 8 328 " (cutoff:3.500A) Processing helix chain '8' and resid 335 through 347 removed outlier: 4.561A pdb=" N ALA 8 340 " --> pdb=" O PRO 8 336 " (cutoff:3.500A) Proline residue: 8 341 - end of helix Processing helix chain '8' and resid 353 through 367 Processing helix chain '8' and resid 372 through 384 Processing helix chain '8' and resid 386 through 390 Processing helix chain '8' and resid 393 through 406 Processing helix chain '8' and resid 407 through 409 No H-bonds generated for 'chain '8' and resid 407 through 409' Processing helix chain '8' and resid 410 through 424 Processing helix chain '8' and resid 428 through 442 removed outlier: 4.072A pdb=" N TYR 8 442 " --> pdb=" O THR 8 438 " (cutoff:3.500A) Processing helix chain '8' and resid 446 through 461 Proline residue: 8 452 - end of helix removed outlier: 3.634A pdb=" N ILE 8 459 " --> pdb=" O MET 8 455 " (cutoff:3.500A) removed outlier: 4.389A 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 483 through 498 Processing helix chain '8' and resid 501 through 517 removed outlier: 4.135A pdb=" N TYR 8 505 " --> pdb=" O ASP 8 501 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN 8 514 " --> pdb=" O SER 8 510 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE 8 515 " --> pdb=" O ARG 8 511 " (cutoff:3.500A) Processing helix chain '8' and resid 524 through 532 removed outlier: 3.538A pdb=" N VAL 8 529 " --> pdb=" O GLU 8 525 " (cutoff:3.500A) Processing helix chain '10' and resid 117 through 141 removed outlier: 4.166A pdb=" N ALA10 121 " --> pdb=" O THR10 117 " (cutoff:3.500A) removed outlier: 4.025A 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: 3.861A pdb=" N ARG10 188 " --> pdb=" O PRO10 184 " (cutoff:3.500A) Processing helix chain '10' and resid 191 through 207 removed outlier: 3.767A pdb=" N LYS10 205 " --> pdb=" O THR10 201 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU10 206 " --> pdb=" O THR10 202 " (cutoff:3.500A) Processing helix chain '10' and resid 211 through 233 removed outlier: 3.724A pdb=" N MET10 221 " --> pdb=" O ALA10 217 " (cutoff:3.500A) Processing helix chain '10' and resid 236 through 249 removed outlier: 4.064A 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: 3.788A 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: 3.747A 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: 3.507A pdb=" N LEU10 325 " --> pdb=" O LEU10 321 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.670A pdb=" N ALA10 348 " --> pdb=" O LEU10 344 " (cutoff:3.500A) Processing helix chain '10' and resid 356 through 370 removed outlier: 3.909A pdb=" N ALA10 361 " --> pdb=" O PRO10 357 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR10 362 " --> pdb=" O HIS10 358 " (cutoff:3.500A) Processing helix chain '10' and resid 374 through 387 removed outlier: 3.932A 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 437 removed outlier: 3.634A pdb=" N ILE10 434 " --> pdb=" O MET10 430 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG10 437 " --> pdb=" O GLN10 433 " (cutoff:3.500A) Processing helix chain '10' and resid 445 through 459 removed outlier: 3.883A pdb=" N ILE10 449 " --> pdb=" O ALA10 445 " (cutoff:3.500A) Processing helix chain '10' and resid 464 through 486 removed outlier: 3.781A pdb=" N ASP10 477 " --> pdb=" O SER10 473 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET10 478 " --> pdb=" O GLN10 474 " (cutoff:3.500A) Processing helix chain '10' and resid 502 through 517 Processing helix chain '10' and resid 521 through 535 removed outlier: 3.579A pdb=" N SER10 525 " --> pdb=" O ALA10 521 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN10 526 " --> pdb=" O PRO10 522 " (cutoff:3.500A) Processing helix chain '14' and resid 49 through 53 Processing helix chain '14' and resid 66 through 70 removed outlier: 4.054A pdb=" N PHE14 70 " --> pdb=" O VAL14 67 " (cutoff:3.500A) Processing helix chain '14' and resid 76 through 87 removed outlier: 3.571A pdb=" N VAL14 80 " --> pdb=" O SER14 76 " (cutoff:3.500A) Processing helix chain '14' and resid 97 through 111 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: 3.622A pdb=" N ILE14 154 " --> pdb=" O MET14 150 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR14 155 " --> pdb=" O HIS14 151 " (cutoff:3.500A) Processing helix chain '14' and resid 156 through 167 removed outlier: 4.030A pdb=" N ALA14 162 " --> pdb=" O THR14 158 " (cutoff:3.500A) Processing helix chain '14' and resid 194 through 199 Processing helix chain '14' and resid 249 through 255 Processing helix chain '14' and resid 256 through 260 Processing helix chain '14' and resid 262 through 272 Processing sheet with id=AA1, first strand: chain '5' and resid 57 through 61 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 131 through 132 Processing sheet with id=AA4, first strand: chain '5' and resid 185 through 188 removed outlier: 5.976A pdb=" N LEU 5 193 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU 5 222 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 6.493A 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 removed outlier: 6.518A pdb=" N VAL 5 240 " --> pdb=" O ILE 5 261 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL 5 263 " --> pdb=" O VAL 5 240 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL 5 242 " --> pdb=" O VAL 5 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '14' and resid 88 through 90 removed outlier: 6.318A pdb=" N VAL14 304 " --> pdb=" O MET14 181 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET14 181 " --> pdb=" O VAL14 304 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS14 306 " --> pdb=" O VAL14 179 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL14 179 " --> pdb=" O CYS14 306 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE14 308 " --> pdb=" O ASP14 177 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP14 177 " --> pdb=" O PHE14 308 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS14 310 " --> pdb=" O TRP14 175 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA14 126 " --> pdb=" O GLN14 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '14' and resid 88 through 90 removed outlier: 6.318A pdb=" N VAL14 304 " --> pdb=" O MET14 181 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET14 181 " --> pdb=" O VAL14 304 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS14 306 " --> pdb=" O VAL14 179 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL14 179 " --> pdb=" O CYS14 306 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE14 308 " --> pdb=" O ASP14 177 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP14 177 " --> pdb=" O PHE14 308 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS14 310 " --> pdb=" O TRP14 175 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL14 172 " --> pdb=" O VAL14 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '14' and resid 190 through 193 removed outlier: 4.372A pdb=" N TRP14 192 " --> pdb=" O PHE14 293 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE14 293 " --> pdb=" O TRP14 192 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4397 1.33 - 1.46: 3466 1.46 - 1.58: 9306 1.58 - 1.70: 64 1.70 - 1.82: 195 Bond restraints: 17428 Sorted by residual: bond pdb=" N PRO 8 521 " pdb=" CD PRO 8 521 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.46e+01 bond pdb=" N PRO 8 524 " pdb=" CD PRO 8 524 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.15e+01 bond pdb=" N VAL14 38 " pdb=" CA VAL14 38 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.10e-02 8.26e+03 7.94e+00 bond pdb=" CA ASN14 206 " pdb=" C ASN14 206 " ideal model delta sigma weight residual 1.531 1.501 0.030 1.15e-02 7.56e+03 6.99e+00 bond pdb=" CA ASP14 66 " pdb=" C ASP14 66 " ideal model delta sigma weight residual 1.528 1.493 0.036 1.38e-02 5.25e+03 6.70e+00 ... (remaining 17423 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.47: 509 105.47 - 112.67: 9272 112.67 - 119.86: 5912 119.86 - 127.06: 7818 127.06 - 134.25: 248 Bond angle restraints: 23759 Sorted by residual: angle pdb=" N VAL14 205 " pdb=" CA VAL14 205 " pdb=" C VAL14 205 " ideal model delta sigma weight residual 107.37 102.20 5.17 1.42e+00 4.96e-01 1.32e+01 angle pdb=" N GLN 5 75 " pdb=" CA GLN 5 75 " pdb=" C GLN 5 75 " ideal model delta sigma weight residual 111.14 114.94 -3.80 1.08e+00 8.57e-01 1.24e+01 angle pdb=" N VAL 5 72 " pdb=" CA VAL 5 72 " pdb=" C VAL 5 72 " ideal model delta sigma weight residual 111.09 115.35 -4.26 1.25e+00 6.40e-01 1.16e+01 angle pdb=" C3' U g -2 " pdb=" O3' U g -2 " pdb=" P U g -1 " ideal model delta sigma weight residual 120.20 125.31 -5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N MET 5 76 " pdb=" CA MET 5 76 " pdb=" C MET 5 76 " ideal model delta sigma weight residual 108.96 113.96 -5.00 1.49e+00 4.50e-01 1.13e+01 ... (remaining 23754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 10191 35.40 - 70.79: 356 70.79 - 106.19: 25 106.19 - 141.58: 1 141.58 - 176.98: 5 Dihedral angle restraints: 10578 sinusoidal: 4542 harmonic: 6036 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 41.85 158.15 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U g -2 " pdb=" C1' U g -2 " pdb=" N1 U g -2 " pdb=" C2 U g -2 " ideal model delta sinusoidal sigma weight residual 232.00 64.45 167.55 1 1.70e+01 3.46e-03 6.57e+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 -60.14 -99.86 1 1.50e+01 4.44e-03 5.00e+01 ... (remaining 10575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1939 0.035 - 0.071: 604 0.071 - 0.106: 135 0.106 - 0.141: 32 0.141 - 0.177: 7 Chirality restraints: 2717 Sorted by residual: 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 -2.57 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" C1' U m 105 " pdb=" O4' U m 105 " pdb=" C2' U m 105 " pdb=" N1 U m 105 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.35e-01 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 -2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 2714 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU10 421 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO10 422 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO10 422 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO10 422 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR10 372 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C THR10 372 " 0.044 2.00e-02 2.50e+03 pdb=" O THR10 372 " -0.016 2.00e-02 2.50e+03 pdb=" N MET10 373 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR 6 465 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO 6 466 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO 6 466 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO 6 466 " 0.035 5.00e-02 4.00e+02 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 933 2.73 - 3.27: 17095 3.27 - 3.82: 27834 3.82 - 4.36: 33348 4.36 - 4.90: 58429 Nonbonded interactions: 137639 Sorted by model distance: nonbonded pdb=" O ASN10 419 " pdb=" ND2 ASN10 419 " model vdw 2.191 2.520 nonbonded pdb=" O HIS14 118 " pdb=" OG1 THR14 121 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR14 61 " pdb=" O ASP14 152 " model vdw 2.224 2.440 nonbonded pdb=" OP2 U g -13 " pdb=" NH1 ARG 5 21 " model vdw 2.229 2.520 nonbonded pdb=" O4 U g -14 " pdb=" NH2 ARG 6 215 " model vdw 2.243 2.520 ... (remaining 137634 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: 0.710 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: 4.650 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 49.700 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.003 0.069 17428 Z= 0.178 Angle : 0.548 10.727 23759 Z= 0.307 Chirality : 0.037 0.177 2717 Planarity : 0.005 0.065 2956 Dihedral : 17.655 176.977 6660 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.90 % Allowed : 12.38 % Favored : 86.72 % 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: 0.86 (0.19), residues: 2047 helix: 1.34 (0.15), residues: 1242 sheet: 0.21 (0.55), residues: 93 loop : -0.68 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 PHE 0.030 0.001 PHE 8 83 TYR 0.011 0.001 TYR14 176 ARG 0.009 0.000 ARG 8 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 237 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 195 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (p) REVERT: 6 250 MET cc_start: 0.7141 (mtt) cc_final: 0.6820 (mtp) REVERT: 10 466 LYS cc_start: 0.7940 (tttm) cc_final: 0.7508 (ptmm) REVERT: 14 107 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8320 (mm-30) outliers start: 16 outliers final: 3 residues processed: 245 average time/residue: 0.3300 time to fit residues: 117.0229 Evaluate side-chains 211 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 76 MET Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 8 residue 469 ARG Chi-restraints excluded: chain 14 residue 249 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 381 HIS 10 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17428 Z= 0.246 Angle : 0.526 9.926 23759 Z= 0.272 Chirality : 0.039 0.174 2717 Planarity : 0.004 0.056 2956 Dihedral : 13.789 179.233 2725 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.92 % Allowed : 13.00 % Favored : 85.08 % 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: 1.06 (0.19), residues: 2047 helix: 1.47 (0.15), residues: 1278 sheet: 0.18 (0.55), residues: 93 loop : -0.65 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 151 PHE 0.026 0.002 PHE 8 83 TYR 0.014 0.001 TYR14 176 ARG 0.004 0.000 ARG 8 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 221 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7226 (mtp-110) cc_final: 0.6907 (mtp-110) REVERT: 8 306 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7858 (t80) REVERT: 8 345 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8842 (mp) REVERT: 8 475 ILE cc_start: 0.8771 (mm) cc_final: 0.8539 (mt) REVERT: 10 173 MET cc_start: 0.8716 (mmm) cc_final: 0.8069 (tpt) REVERT: 10 276 MET cc_start: 0.8871 (tpp) cc_final: 0.8310 (ttp) REVERT: 10 381 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8384 (mp) REVERT: 10 466 LYS cc_start: 0.7931 (tttm) cc_final: 0.7648 (ptmm) REVERT: 14 107 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8289 (mm-30) outliers start: 34 outliers final: 12 residues processed: 245 average time/residue: 0.3212 time to fit residues: 115.2610 Evaluate side-chains 222 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 419 THR Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 477 ASP Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 123 ASN Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 249 ASP Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 51 optimal weight: 0.1980 chunk 187 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 75 GLN ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17428 Z= 0.227 Angle : 0.506 8.897 23759 Z= 0.258 Chirality : 0.038 0.174 2717 Planarity : 0.004 0.051 2956 Dihedral : 13.606 179.877 2717 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.20 % Allowed : 13.91 % Favored : 83.89 % 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: 1.17 (0.19), residues: 2047 helix: 1.60 (0.14), residues: 1284 sheet: 0.03 (0.54), residues: 94 loop : -0.68 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP14 175 HIS 0.004 0.001 HIS14 201 PHE 0.025 0.001 PHE 8 83 TYR 0.011 0.001 TYR10 200 ARG 0.008 0.000 ARG 6 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: 5 125 ARG cc_start: 0.7275 (mtp-110) cc_final: 0.6756 (mtm110) REVERT: 6 250 MET cc_start: 0.7243 (mtt) cc_final: 0.6899 (mtp) REVERT: 8 306 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7695 (t80) REVERT: 8 345 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8802 (mp) REVERT: 8 382 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8925 (mp) REVERT: 10 140 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6406 (tp) REVERT: 10 173 MET cc_start: 0.8746 (mmm) cc_final: 0.8232 (tpt) REVERT: 10 276 MET cc_start: 0.8843 (tpp) cc_final: 0.8324 (ttp) REVERT: 10 335 ASP cc_start: 0.8713 (p0) cc_final: 0.8266 (m-30) REVERT: 10 381 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8341 (mp) REVERT: 14 107 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8334 (mm-30) outliers start: 39 outliers final: 22 residues processed: 239 average time/residue: 0.3293 time to fit residues: 114.8416 Evaluate side-chains 230 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 419 THR Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 493 ASP Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 48 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 167 THR Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 528 GLN Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 182 THR Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 439 ASP Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 10 residue 519 ASP Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 127 ASN 5 151 HIS ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 329 GLN 10 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 17428 Z= 0.496 Angle : 0.671 8.866 23759 Z= 0.343 Chirality : 0.045 0.177 2717 Planarity : 0.005 0.054 2956 Dihedral : 13.691 170.802 2715 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.71 % Allowed : 15.38 % Favored : 81.91 % 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: 0.58 (0.18), residues: 2047 helix: 1.14 (0.14), residues: 1275 sheet: -0.40 (0.51), residues: 101 loop : -0.87 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 8 447 HIS 0.007 0.002 HIS10 246 PHE 0.024 0.002 PHE 8 83 TYR 0.022 0.002 TYR14 176 ARG 0.005 0.001 ARG 6 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 201 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: 6 370 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7794 (ttm170) REVERT: 8 140 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8365 (mtmm) REVERT: 8 251 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7777 (mt-10) REVERT: 8 306 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.7742 (t80) REVERT: 8 345 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8850 (mp) REVERT: 8 382 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8902 (mp) REVERT: 8 495 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7659 (mmp80) REVERT: 10 161 PHE cc_start: 0.6833 (m-80) cc_final: 0.6620 (m-80) REVERT: 10 173 MET cc_start: 0.8859 (mmm) cc_final: 0.8054 (tpt) REVERT: 10 276 MET cc_start: 0.8901 (tpp) cc_final: 0.8462 (ttp) REVERT: 10 356 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8326 (p) REVERT: 10 381 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8498 (mp) REVERT: 10 532 PHE cc_start: 0.8296 (m-10) cc_final: 0.7958 (m-10) outliers start: 48 outliers final: 27 residues processed: 237 average time/residue: 0.3382 time to fit residues: 115.0813 Evaluate side-chains 229 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 5 residue 134 LEU Chi-restraints excluded: chain 6 residue 212 THR Chi-restraints excluded: chain 6 residue 419 THR Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 453 LEU Chi-restraints excluded: chain 6 residue 493 ASP Chi-restraints excluded: chain 7 residue 132 SER Chi-restraints excluded: chain 8 residue 48 THR Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 167 THR Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 327 VAL Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 182 THR Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 333 VAL Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 439 ASP Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 10 residue 467 CYS Chi-restraints excluded: chain 14 residue 190 VAL Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 329 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 136 ASN 10 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17428 Z= 0.175 Angle : 0.491 8.464 23759 Z= 0.254 Chirality : 0.038 0.177 2717 Planarity : 0.004 0.051 2956 Dihedral : 13.482 177.194 2715 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.09 % Allowed : 16.45 % Favored : 81.46 % 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: 1.02 (0.19), residues: 2047 helix: 1.54 (0.15), residues: 1276 sheet: -0.39 (0.52), residues: 96 loop : -0.81 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP14 175 HIS 0.007 0.001 HIS 5 151 PHE 0.019 0.001 PHE 8 83 TYR 0.013 0.001 TYR10 200 ARG 0.003 0.000 ARG 8 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 1.951 Fit side-chains REVERT: 7 143 LYS cc_start: 0.7855 (mttm) cc_final: 0.7575 (ttpp) REVERT: 8 251 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7698 (mt-10) REVERT: 8 306 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.7624 (t80) REVERT: 8 345 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8773 (mp) REVERT: 8 382 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8852 (mp) REVERT: 8 495 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7453 (mmp80) REVERT: 10 139 GLN cc_start: 0.6705 (tp40) cc_final: 0.6446 (mt0) REVERT: 10 276 MET cc_start: 0.8750 (tpp) cc_final: 0.8494 (ttp) REVERT: 10 335 ASP cc_start: 0.8807 (p0) cc_final: 0.8188 (m-30) REVERT: 10 356 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8252 (p) REVERT: 10 381 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8403 (mp) outliers start: 37 outliers final: 20 residues processed: 223 average time/residue: 0.3246 time to fit residues: 104.9662 Evaluate side-chains 215 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 313 ASP Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 493 ASP Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 132 GLU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 167 THR Chi-restraints excluded: chain 8 residue 180 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 182 THR Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 439 ASP Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 249 ASP Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 0.0010 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17428 Z= 0.178 Angle : 0.476 8.680 23759 Z= 0.245 Chirality : 0.037 0.174 2717 Planarity : 0.004 0.051 2956 Dihedral : 13.359 179.506 2715 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.04 % Allowed : 16.56 % Favored : 81.40 % 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: 1.26 (0.19), residues: 2047 helix: 1.75 (0.15), residues: 1280 sheet: -0.29 (0.53), residues: 96 loop : -0.75 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP14 175 HIS 0.004 0.001 HIS10 246 PHE 0.016 0.001 PHE 8 83 TYR 0.012 0.001 TYR10 200 ARG 0.003 0.000 ARG 6 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 1.901 Fit side-chains REVERT: 5 125 ARG cc_start: 0.7469 (mtp-110) cc_final: 0.6898 (mtm110) REVERT: 7 143 LYS cc_start: 0.7809 (mttm) cc_final: 0.7578 (ttpp) REVERT: 8 251 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7663 (mt-10) REVERT: 8 306 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.7692 (t80) REVERT: 8 345 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8765 (mp) REVERT: 8 382 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8848 (mp) REVERT: 8 495 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7456 (mmp80) REVERT: 10 276 MET cc_start: 0.8777 (tpp) cc_final: 0.8370 (ttp) REVERT: 10 335 ASP cc_start: 0.8820 (p0) cc_final: 0.8245 (m-30) REVERT: 10 356 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8271 (p) REVERT: 10 381 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8416 (mp) outliers start: 36 outliers final: 20 residues processed: 223 average time/residue: 0.3218 time to fit residues: 105.2370 Evaluate side-chains 214 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 453 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 167 THR Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 327 VAL Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 182 THR Chi-restraints excluded: chain 10 residue 269 SER Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 249 ASP Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 0.0670 chunk 111 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17428 Z= 0.159 Angle : 0.463 8.628 23759 Z= 0.238 Chirality : 0.037 0.174 2717 Planarity : 0.004 0.050 2956 Dihedral : 13.225 178.007 2715 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.70 % Allowed : 16.96 % Favored : 81.35 % 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: 1.40 (0.19), residues: 2047 helix: 1.85 (0.15), residues: 1280 sheet: -0.27 (0.56), residues: 91 loop : -0.69 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 PHE 0.015 0.001 PHE 8 83 TYR 0.011 0.001 TYR10 200 ARG 0.002 0.000 ARG 8 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.854 Fit side-chains REVERT: 5 125 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.6916 (mtm110) REVERT: 7 143 LYS cc_start: 0.7839 (mttm) cc_final: 0.7548 (ttpp) REVERT: 8 251 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7658 (mt-10) REVERT: 8 306 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.7643 (t80) REVERT: 8 345 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8756 (mp) REVERT: 8 382 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8802 (mp) REVERT: 8 495 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7503 (mmp80) REVERT: 10 276 MET cc_start: 0.8741 (tpp) cc_final: 0.8350 (ttp) REVERT: 10 335 ASP cc_start: 0.8817 (p0) cc_final: 0.8236 (m-30) REVERT: 10 344 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8775 (mp) REVERT: 10 381 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8391 (mp) outliers start: 30 outliers final: 22 residues processed: 216 average time/residue: 0.3316 time to fit residues: 105.2938 Evaluate side-chains 215 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 57 LYS Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 313 ASP Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 167 THR Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 327 VAL Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 182 THR Chi-restraints excluded: chain 10 residue 269 SER Chi-restraints excluded: chain 10 residue 344 LEU Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 439 ASP Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 249 ASP Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17428 Z= 0.242 Angle : 0.504 8.846 23759 Z= 0.258 Chirality : 0.039 0.174 2717 Planarity : 0.004 0.051 2956 Dihedral : 13.188 179.880 2715 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.09 % Allowed : 16.90 % Favored : 81.01 % 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: 1.30 (0.19), residues: 2047 helix: 1.74 (0.15), residues: 1284 sheet: -0.26 (0.52), residues: 96 loop : -0.68 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP14 175 HIS 0.005 0.001 HIS10 246 PHE 0.015 0.001 PHE 8 83 TYR 0.014 0.001 TYR14 176 ARG 0.006 0.000 ARG 5 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.917 Fit side-chains REVERT: 5 125 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7041 (mtm110) REVERT: 6 301 MET cc_start: 0.9066 (mmm) cc_final: 0.8838 (mmm) REVERT: 7 143 LYS cc_start: 0.7848 (mttm) cc_final: 0.7594 (ttpp) REVERT: 8 125 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8308 (m-40) REVERT: 8 251 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7681 (mt-10) REVERT: 8 306 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7650 (t80) REVERT: 8 345 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8763 (mp) REVERT: 8 382 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8817 (mp) REVERT: 8 495 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7538 (mmp80) REVERT: 10 134 ASP cc_start: 0.6997 (m-30) cc_final: 0.6702 (m-30) REVERT: 10 276 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8411 (ttp) REVERT: 10 335 ASP cc_start: 0.8871 (p0) cc_final: 0.8254 (m-30) REVERT: 10 344 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8777 (mp) REVERT: 10 356 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8329 (p) REVERT: 10 381 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8414 (mp) outliers start: 37 outliers final: 26 residues processed: 218 average time/residue: 0.3219 time to fit residues: 103.3881 Evaluate side-chains 226 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 313 ASP Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 453 LEU Chi-restraints excluded: chain 6 residue 493 ASP Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 125 ASN Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 167 THR Chi-restraints excluded: chain 8 residue 220 MET Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 327 VAL Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 182 THR Chi-restraints excluded: chain 10 residue 269 SER Chi-restraints excluded: chain 10 residue 276 MET Chi-restraints excluded: chain 10 residue 344 LEU Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 439 ASP Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 249 ASP Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 293 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 1.9990 chunk 190 optimal weight: 0.0270 chunk 173 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17428 Z= 0.155 Angle : 0.464 9.006 23759 Z= 0.238 Chirality : 0.037 0.175 2717 Planarity : 0.004 0.050 2956 Dihedral : 13.069 178.174 2715 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.87 % Allowed : 17.07 % Favored : 81.06 % 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: 1.45 (0.19), residues: 2047 helix: 1.88 (0.15), residues: 1282 sheet: -0.26 (0.53), residues: 96 loop : -0.63 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 PHE 0.014 0.001 PHE 6 382 TYR 0.011 0.001 TYR10 200 ARG 0.006 0.000 ARG 6 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 1.823 Fit side-chains REVERT: 5 125 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.6919 (mtm110) REVERT: 6 301 MET cc_start: 0.9095 (mmm) cc_final: 0.8864 (mmm) REVERT: 7 143 LYS cc_start: 0.7837 (mttm) cc_final: 0.7556 (ttpp) REVERT: 8 125 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8279 (m-40) REVERT: 8 251 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7750 (mt-10) REVERT: 8 306 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7625 (t80) REVERT: 8 345 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8752 (mp) REVERT: 8 382 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8828 (mp) REVERT: 8 495 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7500 (mmp80) REVERT: 10 276 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8358 (ttp) REVERT: 10 335 ASP cc_start: 0.8843 (p0) cc_final: 0.8271 (m-30) REVERT: 10 344 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8773 (mp) REVERT: 10 356 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8306 (p) REVERT: 10 381 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8379 (mp) REVERT: 14 259 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6841 (mt-10) outliers start: 33 outliers final: 22 residues processed: 223 average time/residue: 0.3189 time to fit residues: 104.4048 Evaluate side-chains 222 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 313 ASP Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 453 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 125 ASN Chi-restraints excluded: chain 8 residue 142 MET Chi-restraints excluded: chain 8 residue 167 THR Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 327 VAL Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 182 THR Chi-restraints excluded: chain 10 residue 269 SER Chi-restraints excluded: chain 10 residue 276 MET Chi-restraints excluded: chain 10 residue 344 LEU Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 249 ASP Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 293 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.9990 chunk 195 optimal weight: 0.0370 chunk 119 optimal weight: 0.5980 chunk 92 optimal weight: 0.0870 chunk 136 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17428 Z= 0.128 Angle : 0.449 8.875 23759 Z= 0.230 Chirality : 0.036 0.175 2717 Planarity : 0.004 0.050 2956 Dihedral : 12.966 176.592 2715 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.64 % Allowed : 17.58 % Favored : 80.78 % 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 (0.19), residues: 2047 helix: 2.00 (0.15), residues: 1282 sheet: -0.28 (0.52), residues: 98 loop : -0.57 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 PHE 0.016 0.001 PHE10 532 TYR 0.009 0.001 TYR10 200 ARG 0.005 0.000 ARG 5 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 2.284 Fit side-chains REVERT: 5 125 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.6919 (mtm110) REVERT: 7 143 LYS cc_start: 0.7834 (mttm) cc_final: 0.7562 (ttpp) REVERT: 8 251 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7657 (mt-10) REVERT: 8 306 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7643 (t80) REVERT: 8 327 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8746 (p) REVERT: 8 345 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8756 (mp) REVERT: 8 382 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8787 (mp) REVERT: 8 495 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7504 (mmp80) REVERT: 10 276 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8312 (ttp) REVERT: 10 335 ASP cc_start: 0.8808 (p0) cc_final: 0.8279 (m-30) REVERT: 10 344 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8736 (mp) REVERT: 10 356 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8338 (p) REVERT: 10 381 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8381 (mp) outliers start: 29 outliers final: 14 residues processed: 223 average time/residue: 0.3299 time to fit residues: 108.1559 Evaluate side-chains 219 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 97 GLU Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 86 MET Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 119 LEU Chi-restraints excluded: chain 8 residue 249 ILE Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 327 VAL Chi-restraints excluded: chain 8 residue 345 ILE Chi-restraints excluded: chain 8 residue 382 ILE Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 495 ARG Chi-restraints excluded: chain 10 residue 114 VAL Chi-restraints excluded: chain 10 residue 269 SER Chi-restraints excluded: chain 10 residue 276 MET Chi-restraints excluded: chain 10 residue 344 LEU Chi-restraints excluded: chain 10 residue 356 THR Chi-restraints excluded: chain 10 residue 381 LEU Chi-restraints excluded: chain 10 residue 434 ILE Chi-restraints excluded: chain 10 residue 441 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 226 LEU Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.130682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.106634 restraints weight = 20251.102| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.23 r_work: 0.2938 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17428 Z= 0.201 Angle : 0.483 7.524 23759 Z= 0.247 Chirality : 0.038 0.175 2717 Planarity : 0.004 0.050 2956 Dihedral : 12.982 178.713 2715 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.58 % Allowed : 17.86 % Favored : 80.55 % 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: 1.49 (0.19), residues: 2047 helix: 1.89 (0.15), residues: 1288 sheet: -0.27 (0.55), residues: 93 loop : -0.58 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP14 175 HIS 0.004 0.001 HIS 5 214 PHE 0.027 0.001 PHE10 532 TYR 0.013 0.001 TYR14 176 ARG 0.004 0.000 ARG 5 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3455.43 seconds wall clock time: 63 minutes 38.79 seconds (3818.79 seconds total)