Starting phenix.real_space_refine on Sun Jul 21 16:56:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yle_10836/07_2024/6yle_10836.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yle_10836/07_2024/6yle_10836.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/6yle_10836/07_2024/6yle_10836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yle_10836/07_2024/6yle_10836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yle_10836/07_2024/6yle_10836.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yle_10836/07_2024/6yle_10836.cif" } 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= 0.004 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 9933 2.51 5 N 2535 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C GLU 512": "OE1" <-> "OE2" Residue "C ARG 561": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 420": "OE1" <-> "OE2" Residue "D PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D ARG 561": "NH1" <-> "NH2" Residue "D GLU 567": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "K GLU 258": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15345 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3139 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain breaks: 9 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3260 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 14, 'TRANS': 400} Chain breaks: 6 Chain: "C" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4352 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 27, 'TRANS': 517} Chain breaks: 4 Chain: "D" Number of atoms: 4380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4380 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 27, 'TRANS': 519} Chain breaks: 2 Chain: "K" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 214 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Time building chain proxies: 8.92, per 1000 atoms: 0.58 Number of scatterers: 15345 At special positions: 0 Unit cell: (113.313, 114.372, 111.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 2816 8.00 N 2535 7.00 C 9933 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: 5.99 Conformation dependent library (CDL) restraints added in 2.6 seconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3678 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 20 sheets defined 44.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 169 through 172 removed outlier: 3.921A pdb=" N VAL A 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.574A pdb=" N GLU A 461 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 462' Processing helix chain 'A' and resid 472 through 485 removed outlier: 4.229A pdb=" N TYR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.941A pdb=" N SER B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.909A pdb=" N SER B 485 " --> pdb=" O LYS B 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 14 removed outlier: 3.687A pdb=" N LEU C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 4.823A pdb=" N THR C 25 " --> pdb=" O ASN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 6.077A pdb=" N VAL C 34 " --> pdb=" O ARG C 31 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 58 removed outlier: 3.764A pdb=" N SER C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 78 Processing helix chain 'C' and resid 78 through 103 removed outlier: 3.606A pdb=" N LEU C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN C 88 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C 103 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 142 through 158 removed outlier: 4.485A pdb=" N LYS C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.501A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Proline residue: C 166 - end of helix Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.886A pdb=" N VAL C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.661A pdb=" N GLU C 263 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.789A pdb=" N TYR C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 278 " --> pdb=" O TYR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 308 Processing helix chain 'C' and resid 309 through 326 removed outlier: 4.244A pdb=" N LEU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 364 through 391 removed outlier: 4.046A pdb=" N THR C 372 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Proline residue: C 375 - end of helix removed outlier: 3.521A pdb=" N GLN C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 401 through 411 removed outlier: 3.585A pdb=" N SER C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 430 through 448 removed outlier: 4.218A pdb=" N HIS C 446 " --> pdb=" O MET C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 468 removed outlier: 4.436A pdb=" N SER C 458 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 536 removed outlier: 4.020A pdb=" N GLU C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 562 removed outlier: 4.373A pdb=" N ILE C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 579 Processing helix chain 'C' and resid 587 through 595 Processing helix chain 'C' and resid 601 through 608 removed outlier: 3.596A pdb=" N LEU C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 3.666A pdb=" N LEU D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 31 removed outlier: 4.788A pdb=" N THR D 25 " --> pdb=" O ASN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 removed outlier: 4.273A pdb=" N LYS D 42 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 58 Processing helix chain 'D' and resid 62 through 77 Processing helix chain 'D' and resid 78 through 102 removed outlier: 6.717A pdb=" N GLY D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.643A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 132 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 142 through 157 removed outlier: 3.682A pdb=" N LYS D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix removed outlier: 3.685A pdb=" N LEU D 156 " --> pdb=" O THR D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.935A pdb=" N VAL D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Proline residue: D 166 - end of helix Processing helix chain 'D' and resid 176 through 181 Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.088A pdb=" N VAL D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 241 through 252 Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 307 through 325 removed outlier: 3.610A pdb=" N MET D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.797A pdb=" N VAL D 349 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 391 Proline residue: D 375 - end of helix removed outlier: 3.901A pdb=" N GLY D 381 " --> pdb=" O ILE D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 399 through 406 Processing helix chain 'D' and resid 407 through 411 Processing helix chain 'D' and resid 422 through 427 removed outlier: 3.794A pdb=" N VAL D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 445 removed outlier: 3.759A pdb=" N THR D 435 " --> pdb=" O PHE D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 469 removed outlier: 3.509A pdb=" N GLU D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 537 Processing helix chain 'D' and resid 540 through 562 Processing helix chain 'D' and resid 566 through 579 Processing helix chain 'D' and resid 589 through 597 removed outlier: 3.626A pdb=" N SER D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 597 " --> pdb=" O SER D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 removed outlier: 3.738A pdb=" N LEU D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU D 606 " --> pdb=" O MET D 602 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS D 607 " --> pdb=" O PHE D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 removed outlier: 4.600A pdb=" N GLY A 13 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN A 4 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 400 " --> pdb=" O GLN A 4 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 6 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 398 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 8 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.665A pdb=" N VAL A 57 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 71 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 85 removed outlier: 3.637A pdb=" N VAL A 85 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 110 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU A 124 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU A 130 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 147 removed outlier: 3.582A pdb=" N CYS A 183 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 198 removed outlier: 3.987A pdb=" N THR A 210 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 216 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP A 225 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU A 250 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N PHE A 312 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR A 253 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU A 314 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR A 255 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 337 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER A 313 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 265 Processing sheet with id=AA7, first strand: chain 'A' and resid 286 through 288 Processing sheet with id=AA8, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.816A pdb=" N LEU A 359 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 380 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU A 372 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 378 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 453 Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 26 removed outlier: 4.065A pdb=" N GLY B 13 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 401 " --> pdb=" O GLN B 4 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 Processing sheet with id=AB3, first strand: chain 'B' and resid 81 through 85 removed outlier: 3.628A pdb=" N VAL B 85 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 110 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 120 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 133 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE B 122 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 129 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 144 through 147 removed outlier: 3.859A pdb=" N CYS B 183 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.961A pdb=" N SER B 216 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 252 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP B 225 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU B 250 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 260 through 265 removed outlier: 6.603A pdb=" N CYS B 280 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 286 through 288 Processing sheet with id=AB8, first strand: chain 'B' and resid 314 through 315 Processing sheet with id=AB9, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.692A pdb=" N GLY B 362 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 350 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 360 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE B 352 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 358 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU B 372 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE B 378 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 450 through 453 Processing sheet with id=AC2, first strand: chain 'C' and resid 471 through 472 673 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4770 1.34 - 1.46: 2924 1.46 - 1.57: 7856 1.57 - 1.69: 1 1.69 - 1.81: 85 Bond restraints: 15636 Sorted by residual: bond pdb=" N SER C 110 " pdb=" CA SER C 110 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" C THR C 328 " pdb=" N PRO C 329 " ideal model delta sigma weight residual 1.331 1.355 -0.024 7.90e-03 1.60e+04 9.16e+00 bond pdb=" C LEU A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.27e-02 6.20e+03 8.98e+00 bond pdb=" C LEU B 190 " pdb=" N PRO B 191 " ideal model delta sigma weight residual 1.331 1.366 -0.035 1.20e-02 6.94e+03 8.50e+00 bond pdb=" C ILE C 538 " pdb=" N LEU C 539 " ideal model delta sigma weight residual 1.331 1.293 0.039 1.54e-02 4.22e+03 6.28e+00 ... (remaining 15631 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.74: 321 105.74 - 112.96: 8374 112.96 - 120.19: 6099 120.19 - 127.42: 6245 127.42 - 134.65: 161 Bond angle restraints: 21200 Sorted by residual: angle pdb=" N GLN C 269 " pdb=" CA GLN C 269 " pdb=" C GLN C 269 " ideal model delta sigma weight residual 111.69 101.06 10.63 1.23e+00 6.61e-01 7.47e+01 angle pdb=" CA VAL B 303 " pdb=" CB VAL B 303 " pdb=" CG2 VAL B 303 " ideal model delta sigma weight residual 110.40 119.51 -9.11 1.70e+00 3.46e-01 2.87e+01 angle pdb=" N LEU B 149 " pdb=" CA LEU B 149 " pdb=" C LEU B 149 " ideal model delta sigma weight residual 110.17 103.03 7.14 1.51e+00 4.39e-01 2.24e+01 angle pdb=" N PRO B 191 " pdb=" CA PRO B 191 " pdb=" C PRO B 191 " ideal model delta sigma weight residual 111.03 118.26 -7.23 1.54e+00 4.22e-01 2.20e+01 angle pdb=" CA VAL B 303 " pdb=" CB VAL B 303 " pdb=" CG1 VAL B 303 " ideal model delta sigma weight residual 110.40 117.87 -7.47 1.70e+00 3.46e-01 1.93e+01 ... (remaining 21195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8276 17.81 - 35.63: 926 35.63 - 53.44: 164 53.44 - 71.26: 44 71.26 - 89.07: 42 Dihedral angle restraints: 9452 sinusoidal: 3810 harmonic: 5642 Sorted by residual: dihedral pdb=" CA ALA A 268 " pdb=" C ALA A 268 " pdb=" N ASP A 269 " pdb=" CA ASP A 269 " ideal model delta harmonic sigma weight residual -180.00 -117.42 -62.58 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA LEU B 205 " pdb=" C LEU B 205 " pdb=" N SER B 206 " pdb=" CA SER B 206 " ideal model delta harmonic sigma weight residual 180.00 139.23 40.77 0 5.00e+00 4.00e-02 6.65e+01 dihedral pdb=" CA SER C 417 " pdb=" C SER C 417 " pdb=" N ASN C 418 " pdb=" CA ASN C 418 " ideal model delta harmonic sigma weight residual 180.00 -143.63 -36.37 0 5.00e+00 4.00e-02 5.29e+01 ... (remaining 9449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 2534 0.349 - 0.699: 0 0.699 - 1.048: 0 1.048 - 1.398: 0 1.398 - 1.747: 1 Chirality restraints: 2535 Sorted by residual: chirality pdb=" CB VAL B 303 " pdb=" CA VAL B 303 " pdb=" CG1 VAL B 303 " pdb=" CG2 VAL B 303 " both_signs ideal model delta sigma weight residual False -2.63 -0.88 -1.75 2.00e-01 2.50e+01 7.63e+01 chirality pdb=" CA GLN C 269 " pdb=" N GLN C 269 " pdb=" C GLN C 269 " pdb=" CB GLN C 269 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LYS D 391 " pdb=" N LYS D 391 " pdb=" C LYS D 391 " pdb=" CB LYS D 391 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2532 not shown) Planarity restraints: 2642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 13 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C GLY B 13 " -0.059 2.00e-02 2.50e+03 pdb=" O GLY B 13 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 14 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 542 " 0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO C 543 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 543 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 543 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 268 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C GLU C 268 " 0.054 2.00e-02 2.50e+03 pdb=" O GLU C 268 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 269 " -0.018 2.00e-02 2.50e+03 ... (remaining 2639 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 76 2.51 - 3.11: 10892 3.11 - 3.70: 22642 3.70 - 4.30: 31744 4.30 - 4.90: 55561 Nonbonded interactions: 120915 Sorted by model distance: nonbonded pdb=" OE1 GLU D 162 " pdb=" OG1 THR D 205 " model vdw 1.910 2.440 nonbonded pdb=" O MET C 131 " pdb=" OG SER C 138 " model vdw 2.137 2.440 nonbonded pdb=" O THR B 208 " pdb=" OG SER B 227 " model vdw 2.138 2.440 nonbonded pdb=" OH TYR D 94 " pdb=" O ALA D 148 " model vdw 2.138 2.440 nonbonded pdb=" OG1 THR B 189 " pdb=" OD2 ASP B 218 " model vdw 2.141 2.440 ... (remaining 120910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 229 or resid 246 through 460 or resid 472 throug \ h 489)) selection = (chain 'B' and (resid 1 through 60 or resid 67 through 299 or resid 310 through \ 317 or resid 331 through 385 or resid 394 through 403 or resid 431 through 442 o \ r resid 447 through 489)) } ncs_group { reference = (chain 'C' and (resid 4 through 469 or resid 520 through 617)) selection = (chain 'D' and (resid 4 through 281 or resid 291 through 351 or resid 363 throug \ h 617)) } 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=0.00 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: 0.490 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: 0.520 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.880 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.009 0.080 15636 Z= 0.611 Angle : 1.051 10.629 21200 Z= 0.578 Chirality : 0.065 1.747 2535 Planarity : 0.007 0.082 2642 Dihedral : 16.797 89.071 5774 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.28 % Allowed : 14.87 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.17 (0.16), residues: 1878 helix: -1.73 (0.15), residues: 762 sheet: -1.54 (0.26), residues: 289 loop : -2.60 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 123 HIS 0.008 0.002 HIS D 24 PHE 0.020 0.002 PHE B 7 TYR 0.016 0.002 TYR C 550 ARG 0.005 0.001 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 322 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.9153 (mp) cc_final: 0.8868 (mp) REVERT: B 119 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7641 (ttpp) REVERT: B 121 TYR cc_start: 0.8279 (m-80) cc_final: 0.7462 (m-80) REVERT: B 154 ILE cc_start: 0.9067 (pt) cc_final: 0.8821 (pt) REVERT: B 364 THR cc_start: 0.8766 (p) cc_final: 0.8471 (m) REVERT: B 439 ILE cc_start: 0.8115 (mp) cc_final: 0.7821 (mp) REVERT: C 64 LEU cc_start: 0.8332 (tp) cc_final: 0.8053 (tp) REVERT: C 110 SER cc_start: 0.6201 (OUTLIER) cc_final: 0.5069 (t) REVERT: C 403 ILE cc_start: 0.8396 (tt) cc_final: 0.8195 (mt) REVERT: D 520 MET cc_start: 0.7131 (mmt) cc_final: 0.6881 (mmp) outliers start: 5 outliers final: 2 residues processed: 325 average time/residue: 0.3256 time to fit residues: 147.0504 Evaluate side-chains 193 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 397 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 1.9990 chunk 144 optimal weight: 0.2980 chunk 79 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 138 HIS B 186 HIS B 188 HIS B 449 HIS C 158 GLN C 452 ASN C 554 GLN D 78 ASN D 242 ASN D 554 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15636 Z= 0.195 Angle : 0.617 7.025 21200 Z= 0.316 Chirality : 0.044 0.166 2535 Planarity : 0.005 0.056 2642 Dihedral : 5.453 45.184 2032 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.77 % Allowed : 15.66 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 1878 helix: -0.13 (0.18), residues: 775 sheet: -1.20 (0.26), residues: 307 loop : -2.21 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 65 HIS 0.003 0.001 HIS A 19 PHE 0.014 0.001 PHE B 7 TYR 0.013 0.001 TYR A 224 ARG 0.004 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8835 (tp) cc_final: 0.8614 (tp) REVERT: A 256 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7685 (p) REVERT: A 349 CYS cc_start: 0.7956 (p) cc_final: 0.7668 (p) REVERT: A 367 LYS cc_start: 0.6711 (ptmt) cc_final: 0.6444 (pttp) REVERT: B 80 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8606 (mttp) REVERT: B 334 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5966 (pmm) REVERT: B 439 ILE cc_start: 0.7882 (mp) cc_final: 0.7576 (mp) REVERT: C 129 ASP cc_start: 0.7380 (m-30) cc_final: 0.7173 (m-30) REVERT: D 388 MET cc_start: 0.8357 (tmm) cc_final: 0.7979 (tmm) REVERT: K 261 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8745 (mmtt) outliers start: 49 outliers final: 27 residues processed: 266 average time/residue: 0.2789 time to fit residues: 110.3993 Evaluate side-chains 202 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 100 HIS B 140 GLN B 377 GLN B 454 GLN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS D 242 ASN D 446 HIS D 449 HIS D 527 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15636 Z= 0.274 Angle : 0.619 7.871 21200 Z= 0.314 Chirality : 0.045 0.168 2535 Planarity : 0.004 0.052 2642 Dihedral : 5.251 48.113 2029 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.62 % Allowed : 16.39 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1878 helix: 0.40 (0.19), residues: 789 sheet: -1.00 (0.27), residues: 316 loop : -1.92 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 65 HIS 0.004 0.001 HIS B 186 PHE 0.014 0.001 PHE B 7 TYR 0.014 0.001 TYR A 224 ARG 0.013 0.001 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 191 time to evaluate : 1.810 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8889 (tp) cc_final: 0.8685 (tp) REVERT: A 256 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7785 (p) REVERT: A 349 CYS cc_start: 0.7855 (p) cc_final: 0.7559 (p) REVERT: B 154 ILE cc_start: 0.9146 (pt) cc_final: 0.8922 (mp) REVERT: B 334 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6121 (pmm) REVERT: B 439 ILE cc_start: 0.7802 (mp) cc_final: 0.7503 (mp) REVERT: C 408 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7223 (tm-30) REVERT: D 140 GLU cc_start: 0.4619 (OUTLIER) cc_final: 0.4284 (mt-10) REVERT: D 520 MET cc_start: 0.7160 (mmt) cc_final: 0.6426 (mmt) REVERT: K 261 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8792 (mmtt) REVERT: K 265 ARG cc_start: 0.4353 (OUTLIER) cc_final: 0.4120 (ppt170) outliers start: 64 outliers final: 38 residues processed: 242 average time/residue: 0.2508 time to fit residues: 92.5654 Evaluate side-chains 208 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 201 GLN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15636 Z= 0.313 Angle : 0.617 8.217 21200 Z= 0.316 Chirality : 0.046 0.175 2535 Planarity : 0.004 0.043 2642 Dihedral : 5.201 49.473 2029 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.96 % Allowed : 17.75 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 1878 helix: 0.78 (0.19), residues: 781 sheet: -0.91 (0.27), residues: 321 loop : -1.72 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 65 HIS 0.006 0.001 HIS A 19 PHE 0.014 0.001 PHE D 433 TYR 0.015 0.001 TYR A 224 ARG 0.003 0.000 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 175 time to evaluate : 1.636 Fit side-chains REVERT: A 75 LEU cc_start: 0.8946 (mt) cc_final: 0.8677 (mt) REVERT: A 130 LEU cc_start: 0.8949 (tp) cc_final: 0.8736 (tp) REVERT: A 256 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8056 (p) REVERT: A 266 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: A 332 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.6362 (t80) REVERT: A 349 CYS cc_start: 0.7637 (p) cc_final: 0.7318 (p) REVERT: B 154 ILE cc_start: 0.9193 (pt) cc_final: 0.8970 (mp) REVERT: B 334 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.6180 (pmm) REVERT: B 439 ILE cc_start: 0.7708 (mp) cc_final: 0.7477 (mp) REVERT: C 408 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7498 (tm-30) REVERT: D 140 GLU cc_start: 0.4715 (OUTLIER) cc_final: 0.4342 (mt-10) REVERT: D 399 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7757 (p90) REVERT: K 252 ASP cc_start: 0.8408 (p0) cc_final: 0.8090 (p0) REVERT: K 261 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8838 (mmtt) REVERT: K 265 ARG cc_start: 0.4388 (OUTLIER) cc_final: 0.4141 (ppt170) outliers start: 70 outliers final: 46 residues processed: 228 average time/residue: 0.2212 time to fit residues: 78.6809 Evaluate side-chains 206 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 153 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 264 THR Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 75 optimal weight: 0.0970 chunk 156 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 87 ASN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS D 192 ASN ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15636 Z= 0.153 Angle : 0.544 7.528 21200 Z= 0.275 Chirality : 0.043 0.190 2535 Planarity : 0.004 0.042 2642 Dihedral : 4.804 49.079 2029 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.05 % Allowed : 19.22 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1878 helix: 1.15 (0.19), residues: 779 sheet: -0.57 (0.28), residues: 317 loop : -1.61 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 65 HIS 0.004 0.001 HIS A 19 PHE 0.011 0.001 PHE B 7 TYR 0.014 0.001 TYR A 224 ARG 0.002 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 1.655 Fit side-chains REVERT: A 130 LEU cc_start: 0.8904 (tp) cc_final: 0.8694 (tp) REVERT: A 266 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: A 332 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.6209 (t80) REVERT: A 349 CYS cc_start: 0.7527 (p) cc_final: 0.7324 (p) REVERT: A 367 LYS cc_start: 0.6601 (ptmt) cc_final: 0.6374 (pttp) REVERT: C 387 ILE cc_start: 0.9208 (mt) cc_final: 0.8901 (mp) REVERT: C 408 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 140 GLU cc_start: 0.4673 (OUTLIER) cc_final: 0.4301 (mt-10) REVERT: D 178 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8944 (m) REVERT: D 403 ILE cc_start: 0.9097 (pt) cc_final: 0.8893 (pt) REVERT: D 520 MET cc_start: 0.7141 (mmt) cc_final: 0.6667 (mmt) REVERT: K 252 ASP cc_start: 0.8348 (p0) cc_final: 0.8007 (p0) REVERT: K 261 LYS cc_start: 0.9302 (mtpt) cc_final: 0.8836 (mmtt) outliers start: 54 outliers final: 29 residues processed: 240 average time/residue: 0.2232 time to fit residues: 84.2970 Evaluate side-chains 204 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 87 ASN B 474 ASN ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15636 Z= 0.219 Angle : 0.566 10.130 21200 Z= 0.286 Chirality : 0.044 0.194 2535 Planarity : 0.004 0.041 2642 Dihedral : 4.736 47.296 2029 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.39 % Allowed : 19.67 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 1878 helix: 1.25 (0.19), residues: 780 sheet: -0.50 (0.28), residues: 310 loop : -1.53 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 65 HIS 0.004 0.001 HIS A 19 PHE 0.013 0.001 PHE D 431 TYR 0.016 0.001 TYR C 159 ARG 0.004 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 175 time to evaluate : 1.929 Fit side-chains REVERT: A 130 LEU cc_start: 0.8928 (tp) cc_final: 0.8712 (tp) REVERT: A 266 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: A 332 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.6228 (t80) REVERT: A 367 LYS cc_start: 0.6682 (ptmt) cc_final: 0.6445 (pttp) REVERT: C 387 ILE cc_start: 0.9175 (mt) cc_final: 0.8822 (mp) REVERT: C 408 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7538 (tm-30) REVERT: D 140 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.4233 (mt-10) REVERT: D 403 ILE cc_start: 0.9121 (pt) cc_final: 0.8913 (pt) REVERT: D 520 MET cc_start: 0.7154 (mmt) cc_final: 0.6622 (mmt) REVERT: K 252 ASP cc_start: 0.8344 (p0) cc_final: 0.8002 (p0) REVERT: K 261 LYS cc_start: 0.9327 (mtpt) cc_final: 0.8854 (mmtt) outliers start: 60 outliers final: 45 residues processed: 224 average time/residue: 0.2405 time to fit residues: 84.3625 Evaluate side-chains 212 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15636 Z= 0.187 Angle : 0.549 10.377 21200 Z= 0.276 Chirality : 0.043 0.191 2535 Planarity : 0.003 0.041 2642 Dihedral : 4.638 48.444 2029 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.22 % Allowed : 19.84 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1878 helix: 1.41 (0.20), residues: 773 sheet: -0.39 (0.28), residues: 315 loop : -1.39 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 65 HIS 0.004 0.001 HIS A 19 PHE 0.013 0.001 PHE B 7 TYR 0.013 0.001 TYR A 224 ARG 0.002 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 179 time to evaluate : 1.933 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8906 (tp) cc_final: 0.8695 (tp) REVERT: A 266 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: A 332 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.6349 (t80) REVERT: A 367 LYS cc_start: 0.6646 (ptmt) cc_final: 0.6399 (pttp) REVERT: C 387 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8753 (mp) REVERT: C 390 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8695 (m) REVERT: C 408 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7551 (tm-30) REVERT: D 140 GLU cc_start: 0.4715 (OUTLIER) cc_final: 0.4289 (mt-10) REVERT: D 520 MET cc_start: 0.7150 (mmt) cc_final: 0.6654 (mmt) REVERT: K 252 ASP cc_start: 0.8331 (p0) cc_final: 0.7976 (p0) REVERT: K 261 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8826 (mmtt) outliers start: 57 outliers final: 40 residues processed: 226 average time/residue: 0.2382 time to fit residues: 84.6500 Evaluate side-chains 213 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 168 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.0070 chunk 109 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 HIS ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15636 Z= 0.145 Angle : 0.542 9.134 21200 Z= 0.272 Chirality : 0.043 0.185 2535 Planarity : 0.003 0.039 2642 Dihedral : 4.444 48.140 2029 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.71 % Allowed : 20.75 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1878 helix: 1.53 (0.20), residues: 772 sheet: -0.26 (0.29), residues: 304 loop : -1.29 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 65 HIS 0.008 0.001 HIS D 85 PHE 0.016 0.001 PHE D 431 TYR 0.012 0.001 TYR A 224 ARG 0.001 0.000 ARG D 584 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 185 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: A 332 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.6351 (t80) REVERT: A 367 LYS cc_start: 0.6641 (ptmt) cc_final: 0.6382 (pttp) REVERT: C 387 ILE cc_start: 0.9091 (mt) cc_final: 0.8690 (mp) REVERT: C 408 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7537 (tm-30) REVERT: D 140 GLU cc_start: 0.4592 (OUTLIER) cc_final: 0.4180 (mt-10) REVERT: D 520 MET cc_start: 0.7115 (mmt) cc_final: 0.6721 (mmt) REVERT: K 252 ASP cc_start: 0.8251 (p0) cc_final: 0.7902 (p0) REVERT: K 261 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8830 (mmtt) outliers start: 48 outliers final: 31 residues processed: 228 average time/residue: 0.2373 time to fit residues: 84.2601 Evaluate side-chains 208 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.0040 chunk 170 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 0.0770 chunk 154 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.0154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 HIS ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15636 Z= 0.159 Angle : 0.556 12.124 21200 Z= 0.275 Chirality : 0.043 0.186 2535 Planarity : 0.003 0.038 2642 Dihedral : 4.403 47.983 2029 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.49 % Allowed : 21.03 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1878 helix: 1.55 (0.20), residues: 774 sheet: -0.17 (0.29), residues: 302 loop : -1.24 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 65 HIS 0.009 0.001 HIS D 85 PHE 0.012 0.001 PHE B 7 TYR 0.013 0.001 TYR A 224 ARG 0.001 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: A 332 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.6347 (t80) REVERT: A 367 LYS cc_start: 0.6669 (ptmt) cc_final: 0.6404 (pttp) REVERT: C 387 ILE cc_start: 0.9024 (mt) cc_final: 0.8666 (mp) REVERT: C 408 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 604 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8854 (tm-30) REVERT: D 140 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.4196 (mt-10) REVERT: D 520 MET cc_start: 0.7107 (mmt) cc_final: 0.6733 (mmt) REVERT: K 252 ASP cc_start: 0.8215 (p0) cc_final: 0.7852 (p0) REVERT: K 261 LYS cc_start: 0.9312 (mtpt) cc_final: 0.8834 (mmtt) outliers start: 44 outliers final: 34 residues processed: 213 average time/residue: 0.2362 time to fit residues: 78.5326 Evaluate side-chains 202 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15636 Z= 0.245 Angle : 0.587 10.172 21200 Z= 0.293 Chirality : 0.045 0.188 2535 Planarity : 0.004 0.039 2642 Dihedral : 4.580 48.717 2029 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.60 % Allowed : 21.09 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1878 helix: 1.51 (0.20), residues: 774 sheet: -0.28 (0.29), residues: 299 loop : -1.22 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 65 HIS 0.008 0.001 HIS D 85 PHE 0.014 0.001 PHE D 431 TYR 0.014 0.001 TYR A 224 ARG 0.002 0.000 ARG D 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 1.607 Fit side-chains REVERT: A 332 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6472 (t80) REVERT: A 367 LYS cc_start: 0.6726 (ptmt) cc_final: 0.6454 (pttp) REVERT: C 387 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8655 (mp) REVERT: C 408 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 604 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8904 (tm-30) REVERT: D 140 GLU cc_start: 0.4834 (OUTLIER) cc_final: 0.4432 (mt-10) REVERT: D 403 ILE cc_start: 0.9074 (pt) cc_final: 0.8816 (pt) REVERT: D 520 MET cc_start: 0.7146 (mmt) cc_final: 0.6669 (mmt) REVERT: K 252 ASP cc_start: 0.8280 (p0) cc_final: 0.7906 (p0) REVERT: K 261 LYS cc_start: 0.9323 (mtpt) cc_final: 0.8834 (mmtt) outliers start: 46 outliers final: 42 residues processed: 204 average time/residue: 0.2381 time to fit residues: 75.9826 Evaluate side-chains 208 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 19 optimal weight: 0.0870 chunk 27 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN C 212 ASN D 69 HIS D 378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.089648 restraints weight = 32941.070| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.67 r_work: 0.3064 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15636 Z= 0.286 Angle : 0.611 10.153 21200 Z= 0.307 Chirality : 0.045 0.189 2535 Planarity : 0.004 0.042 2642 Dihedral : 4.781 49.047 2029 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.94 % Allowed : 20.69 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1878 helix: 1.45 (0.19), residues: 771 sheet: -0.34 (0.29), residues: 302 loop : -1.26 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.007 0.001 HIS D 85 PHE 0.014 0.001 PHE B 7 TYR 0.015 0.001 TYR A 224 ARG 0.003 0.000 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.04 seconds wall clock time: 55 minutes 2.15 seconds (3302.15 seconds total)