Starting phenix.real_space_refine on Fri Jan 19 09:59:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/01_2024/6m5s_30091.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/01_2024/6m5s_30091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/01_2024/6m5s_30091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/01_2024/6m5s_30091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/01_2024/6m5s_30091.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/01_2024/6m5s_30091.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 50 5.16 5 C 7008 2.51 5 N 1996 2.21 5 O 1999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B ASP 495": "OD1" <-> "OD2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 523": "NH1" <-> "NH2" Residue "B ARG 531": "NH1" <-> "NH2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B GLU 605": "OE1" <-> "OE2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "B TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 760": "OD1" <-> "OD2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ASP 49": "OD1" <-> "OD2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ASP 123": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 11055 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 4924 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 30, 'TRANS': 615} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5296 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 35, 'TRANS': 653} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 833 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5857 SG CYS B 121 31.952 45.248 52.606 1.00 29.72 S ATOM 10821 SG CYS C 101 32.764 44.141 55.743 1.00 44.32 S ATOM 6446 SG CYS B 197 53.212 53.899 49.307 1.00 30.65 S ATOM 6464 SG CYS B 200 55.214 54.207 52.200 1.00 34.04 S Time building chain proxies: 5.78, per 1000 atoms: 0.52 Number of scatterers: 11055 At special positions: 0 Unit cell: (108.16, 96.72, 118.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 50 16.00 O 1999 8.00 N 1996 7.00 C 7008 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: 4.36 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B 801 " - pdb=" SG CYS C 101 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 124 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 197 " pdb="ZN ZN B 802 " - pdb=" ND1 HIS B 225 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 200 " 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 54.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 removed outlier: 4.233A pdb=" N LEU A 41 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 42' Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.481A pdb=" N SER A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.761A pdb=" N LYS A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 119 removed outlier: 4.039A pdb=" N ARG A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Proline residue: A 132 - end of helix removed outlier: 3.863A pdb=" N ASN A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.932A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.964A pdb=" N LEU A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 4.421A pdb=" N LEU A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.888A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 293 through 308 removed outlier: 3.977A pdb=" N VAL A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 336 through 340 removed outlier: 4.088A pdb=" N SER A 339 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 374 removed outlier: 3.715A pdb=" N ILE A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.544A pdb=" N ASN A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 418 through 424 removed outlier: 4.536A pdb=" N VAL A 421 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 424 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.553A pdb=" N SER A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 549 through 569 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'B' and resid 6 through 33 removed outlier: 4.024A pdb=" N ARG B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'B' and resid 60 through 70 removed outlier: 4.143A pdb=" N GLY B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.933A pdb=" N THR B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 92 " --> pdb=" O TRP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.607A pdb=" N GLU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.919A pdb=" N PHE B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 removed outlier: 4.094A pdb=" N LEU B 204 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.605A pdb=" N TYR B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 267 removed outlier: 3.859A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.701A pdb=" N LEU B 311 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 313 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 355 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.987A pdb=" N ILE B 381 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.548A pdb=" N GLN B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.503A pdb=" N VAL B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.616A pdb=" N CYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 507 removed outlier: 3.926A pdb=" N ILE B 488 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 501 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.543A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 524 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 560 removed outlier: 4.056A pdb=" N ALA B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 587 removed outlier: 4.549A pdb=" N ALA B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 595 through 608 removed outlier: 3.866A pdb=" N ARG B 602 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 634 removed outlier: 3.581A pdb=" N SER B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 641 through 646 Processing helix chain 'B' and resid 676 through 700 removed outlier: 3.832A pdb=" N ALA B 681 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.786A pdb=" N ILE B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.019A pdb=" N ALA C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 61 through 81 removed outlier: 3.533A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 128 removed outlier: 3.640A pdb=" N GLU C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 removed outlier: 3.941A pdb=" N SER A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 616 through 619 removed outlier: 6.194A pdb=" N VAL A 576 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 503 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG A 528 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY A 527 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 535 " --> pdb=" O GLY A 527 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR A 529 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR A 533 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR A 533 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER A 659 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 535 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU A 661 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 537 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 663 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU A 539 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 707 through 708 removed outlier: 3.691A pdb=" N VAL B 741 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 754 " --> pdb=" O VAL B 741 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1398 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: 3.08 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2256 1.33 - 1.45: 2669 1.45 - 1.57: 6288 1.57 - 1.69: 4 1.69 - 1.81: 71 Bond restraints: 11288 Sorted by residual: bond pdb=" N ARG A 475 " pdb=" CA ARG A 475 " ideal model delta sigma weight residual 1.455 1.491 -0.036 9.60e-03 1.09e+04 1.41e+01 bond pdb=" CA VAL A 525 " pdb=" CB VAL A 525 " ideal model delta sigma weight residual 1.537 1.581 -0.043 1.26e-02 6.30e+03 1.18e+01 bond pdb=" C ARG A 490 " pdb=" O ARG A 490 " ideal model delta sigma weight residual 1.244 1.211 0.034 1.00e-02 1.00e+04 1.12e+01 bond pdb=" CA LEU A 435 " pdb=" C LEU A 435 " ideal model delta sigma weight residual 1.523 1.567 -0.044 1.34e-02 5.57e+03 1.07e+01 bond pdb=" C GLY A 582 " pdb=" O GLY A 582 " ideal model delta sigma weight residual 1.239 1.216 0.023 7.10e-03 1.98e+04 1.03e+01 ... (remaining 11283 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.68: 255 105.68 - 112.80: 5943 112.80 - 119.91: 3811 119.91 - 127.02: 5205 127.02 - 134.13: 122 Bond angle restraints: 15336 Sorted by residual: angle pdb=" N VAL A 477 " pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 111.62 115.81 -4.19 7.90e-01 1.60e+00 2.81e+01 angle pdb=" N ARG A 420 " pdb=" CA ARG A 420 " pdb=" C ARG A 420 " ideal model delta sigma weight residual 111.82 106.51 5.31 1.16e+00 7.43e-01 2.09e+01 angle pdb=" O PRO A 624 " pdb=" C PRO A 624 " pdb=" N PRO A 625 " ideal model delta sigma weight residual 121.31 123.23 -1.92 4.60e-01 4.73e+00 1.75e+01 angle pdb=" N VAL A 656 " pdb=" CA VAL A 656 " pdb=" C VAL A 656 " ideal model delta sigma weight residual 108.11 113.88 -5.77 1.40e+00 5.10e-01 1.70e+01 angle pdb=" N PHE A 573 " pdb=" CA PHE A 573 " pdb=" C PHE A 573 " ideal model delta sigma weight residual 109.07 115.56 -6.49 1.61e+00 3.86e-01 1.62e+01 ... (remaining 15331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5989 17.97 - 35.93: 592 35.93 - 53.90: 128 53.90 - 71.86: 21 71.86 - 89.83: 16 Dihedral angle restraints: 6746 sinusoidal: 2576 harmonic: 4170 Sorted by residual: dihedral pdb=" CA CYS B 223 " pdb=" C CYS B 223 " pdb=" N ASN B 224 " pdb=" CA ASN B 224 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" C VAL A 558 " pdb=" N VAL A 558 " pdb=" CA VAL A 558 " pdb=" CB VAL A 558 " ideal model delta harmonic sigma weight residual -122.00 -133.88 11.88 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CA VAL A 558 " pdb=" CB VAL A 558 " ideal model delta harmonic sigma weight residual 123.40 134.89 -11.49 0 2.50e+00 1.60e-01 2.11e+01 ... (remaining 6743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1556 0.074 - 0.147: 166 0.147 - 0.221: 27 0.221 - 0.295: 7 0.295 - 0.368: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CA VAL A 558 " pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CB VAL A 558 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA VAL A 506 " pdb=" N VAL A 506 " pdb=" C VAL A 506 " pdb=" CB VAL A 506 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1755 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 719 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C ALA A 719 " 0.065 2.00e-02 2.50e+03 pdb=" O ALA A 719 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 720 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 720 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C ALA A 720 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 720 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN A 721 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 724 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 725 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 725 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 725 " 0.030 5.00e-02 4.00e+02 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 112 2.59 - 3.17: 9526 3.17 - 3.75: 16628 3.75 - 4.32: 23015 4.32 - 4.90: 38163 Nonbonded interactions: 87444 Sorted by model distance: nonbonded pdb=" O CYS B 223 " pdb="ZN ZN B 802 " model vdw 2.015 2.230 nonbonded pdb=" OE2 GLU B 30 " pdb=" OG SER B 182 " model vdw 2.208 2.440 nonbonded pdb=" OE1 GLU B 203 " pdb=" NH2 ARG B 221 " model vdw 2.245 2.520 nonbonded pdb=" O GLU B 30 " pdb=" NH1 ARG B 34 " model vdw 2.248 2.520 nonbonded pdb=" CD1 ILE C 17 " pdb=" OE2 GLU C 48 " model vdw 2.256 3.460 ... (remaining 87439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.010 Extract box with map and model: 10.180 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 33.170 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 0.005 0.056 11288 Z= 0.350 Angle : 0.775 8.528 15336 Z= 0.485 Chirality : 0.052 0.368 1758 Planarity : 0.005 0.055 2003 Dihedral : 15.649 89.827 4042 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.23 % Favored : 90.63 % Rotamer: Outliers : 5.29 % Allowed : 17.37 % Favored : 77.34 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.20), residues: 1420 helix: -1.67 (0.18), residues: 677 sheet: -1.46 (0.49), residues: 106 loop : -3.47 (0.21), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 658 HIS 0.009 0.001 HIS A 540 PHE 0.023 0.002 PHE A 634 TYR 0.018 0.002 TYR A 507 ARG 0.005 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 287 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.8085 (t0) cc_final: 0.7739 (t0) REVERT: B 115 MET cc_start: 0.7743 (mmm) cc_final: 0.7425 (tpp) REVERT: B 190 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8362 (pp) REVERT: B 329 PHE cc_start: 0.7239 (t80) cc_final: 0.6802 (t80) REVERT: B 387 SER cc_start: 0.8003 (p) cc_final: 0.7636 (t) REVERT: B 667 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: C 13 LEU cc_start: 0.6179 (mt) cc_final: 0.5923 (mp) outliers start: 60 outliers final: 10 residues processed: 334 average time/residue: 0.2873 time to fit residues: 126.6050 Evaluate side-chains 159 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 761 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 0.0770 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 0.0170 chunk 43 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 133 GLN A 135 ASN A 155 GLN A 211 HIS A 341 ASN A 343 ASN A 351 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 408 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 53 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 195 HIS ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN C 103 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.210 Angle : 0.680 10.476 15336 Z= 0.341 Chirality : 0.043 0.302 1758 Planarity : 0.005 0.040 2003 Dihedral : 5.839 59.517 1601 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.08 % Favored : 90.85 % Rotamer: Outliers : 4.59 % Allowed : 22.75 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.21), residues: 1420 helix: -0.74 (0.19), residues: 691 sheet: -1.25 (0.49), residues: 106 loop : -3.03 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 485 HIS 0.011 0.001 HIS A 601 PHE 0.022 0.002 PHE A 241 TYR 0.016 0.001 TYR A 631 ARG 0.008 0.001 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 153 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.7770 (t0) cc_final: 0.7528 (t0) REVERT: A 357 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6252 (tm-30) REVERT: B 190 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8314 (pp) REVERT: B 329 PHE cc_start: 0.7304 (t80) cc_final: 0.6793 (t80) REVERT: B 333 LEU cc_start: 0.8800 (mt) cc_final: 0.8524 (mt) REVERT: B 485 TRP cc_start: 0.3715 (OUTLIER) cc_final: 0.3306 (m100) REVERT: B 667 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6071 (m-80) REVERT: C 13 LEU cc_start: 0.6213 (mt) cc_final: 0.5848 (mp) outliers start: 52 outliers final: 26 residues processed: 197 average time/residue: 0.2581 time to fit residues: 71.6778 Evaluate side-chains 143 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 485 TRP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 601 HIS Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 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 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 359 ASN A 408 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS B 210 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN B 522 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 HIS B 621 GLN C 126 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11288 Z= 0.251 Angle : 0.666 9.060 15336 Z= 0.336 Chirality : 0.043 0.293 1758 Planarity : 0.005 0.088 2003 Dihedral : 5.463 57.912 1591 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.01 % Favored : 90.92 % Rotamer: Outliers : 4.76 % Allowed : 23.28 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.22), residues: 1420 helix: -0.36 (0.20), residues: 709 sheet: -1.16 (0.49), residues: 114 loop : -2.81 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 658 HIS 0.004 0.001 HIS A 595 PHE 0.031 0.002 PHE A 309 TYR 0.009 0.001 TYR A 631 ARG 0.014 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 122 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7914 (t) REVERT: A 86 ASN cc_start: 0.7773 (t0) cc_final: 0.7537 (t0) REVERT: A 201 LEU cc_start: 0.8833 (tp) cc_final: 0.8311 (mt) REVERT: A 256 PHE cc_start: 0.7612 (m-80) cc_final: 0.7403 (m-80) REVERT: B 158 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8136 (pp) REVERT: B 190 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 329 PHE cc_start: 0.7235 (t80) cc_final: 0.6754 (t80) REVERT: B 485 TRP cc_start: 0.3718 (OUTLIER) cc_final: 0.3451 (m100) REVERT: B 667 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7541 (t80) REVERT: C 13 LEU cc_start: 0.6224 (mt) cc_final: 0.5881 (mp) outliers start: 54 outliers final: 37 residues processed: 165 average time/residue: 0.2078 time to fit residues: 51.1484 Evaluate side-chains 146 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 104 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 485 TRP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 8.9990 chunk 97 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 102 HIS A 408 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11288 Z= 0.181 Angle : 0.624 12.550 15336 Z= 0.309 Chirality : 0.041 0.248 1758 Planarity : 0.004 0.035 2003 Dihedral : 5.234 57.628 1590 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.80 % Favored : 91.13 % Rotamer: Outliers : 4.76 % Allowed : 23.37 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.23), residues: 1420 helix: -0.00 (0.20), residues: 703 sheet: -1.04 (0.50), residues: 114 loop : -2.57 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 658 HIS 0.010 0.001 HIS B 124 PHE 0.031 0.002 PHE A 241 TYR 0.009 0.001 TYR A 214 ARG 0.007 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 122 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.7535 (m-80) cc_final: 0.7323 (m-80) REVERT: A 357 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: B 329 PHE cc_start: 0.7199 (t80) cc_final: 0.6696 (t80) REVERT: B 485 TRP cc_start: 0.3683 (OUTLIER) cc_final: 0.3442 (m100) REVERT: B 667 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: C 13 LEU cc_start: 0.6260 (mt) cc_final: 0.5956 (mp) REVERT: C 49 ASP cc_start: 0.7491 (t0) cc_final: 0.6850 (t0) outliers start: 54 outliers final: 31 residues processed: 164 average time/residue: 0.2149 time to fit residues: 51.9755 Evaluate side-chains 144 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 485 TRP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.0270 chunk 1 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 408 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11288 Z= 0.296 Angle : 0.663 8.625 15336 Z= 0.337 Chirality : 0.043 0.158 1758 Planarity : 0.004 0.036 2003 Dihedral : 5.131 55.910 1587 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.15 % Favored : 90.77 % Rotamer: Outliers : 5.11 % Allowed : 23.72 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1420 helix: 0.17 (0.20), residues: 701 sheet: -1.11 (0.51), residues: 114 loop : -2.44 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 658 HIS 0.014 0.001 HIS A 102 PHE 0.029 0.002 PHE A 241 TYR 0.013 0.002 TYR A 214 ARG 0.008 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 113 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: B 329 PHE cc_start: 0.7252 (t80) cc_final: 0.6792 (t80) REVERT: B 485 TRP cc_start: 0.3620 (OUTLIER) cc_final: 0.3418 (m100) REVERT: B 667 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7644 (t80) outliers start: 58 outliers final: 37 residues processed: 159 average time/residue: 0.1978 time to fit residues: 47.7152 Evaluate side-chains 142 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 102 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 485 TRP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 359 ASN A 408 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11288 Z= 0.319 Angle : 0.686 12.875 15336 Z= 0.346 Chirality : 0.043 0.152 1758 Planarity : 0.005 0.054 2003 Dihedral : 5.233 56.330 1587 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.76 % Allowed : 25.04 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1420 helix: 0.29 (0.20), residues: 704 sheet: -0.80 (0.57), residues: 89 loop : -2.38 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 658 HIS 0.010 0.001 HIS A 102 PHE 0.031 0.002 PHE A 241 TYR 0.017 0.002 TYR A 214 ARG 0.007 0.001 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 119 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: A 328 ASP cc_start: 0.6216 (p0) cc_final: 0.5515 (t0) REVERT: A 416 ASP cc_start: 0.6667 (OUTLIER) cc_final: 0.6454 (p0) REVERT: B 329 PHE cc_start: 0.7310 (t80) cc_final: 0.6908 (t80) REVERT: B 395 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7381 (tp) REVERT: B 667 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7742 (t80) outliers start: 54 outliers final: 38 residues processed: 160 average time/residue: 0.2006 time to fit residues: 47.7357 Evaluate side-chains 148 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.0970 chunk 78 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 595 HIS ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11288 Z= 0.172 Angle : 0.632 15.153 15336 Z= 0.310 Chirality : 0.041 0.158 1758 Planarity : 0.004 0.038 2003 Dihedral : 4.995 57.530 1587 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.31 % Favored : 91.62 % Rotamer: Outliers : 3.53 % Allowed : 26.90 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1420 helix: 0.46 (0.20), residues: 714 sheet: -0.66 (0.58), residues: 89 loop : -2.28 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 485 HIS 0.006 0.001 HIS A 102 PHE 0.030 0.002 PHE A 241 TYR 0.012 0.001 TYR B 731 ARG 0.005 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.7458 (t0) cc_final: 0.7109 (t0) REVERT: A 241 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: A 328 ASP cc_start: 0.5972 (p0) cc_final: 0.5360 (t0) REVERT: A 357 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: A 448 ARG cc_start: 0.6071 (mmt90) cc_final: 0.5632 (tpt170) REVERT: B 158 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8496 (pp) REVERT: B 329 PHE cc_start: 0.7255 (t80) cc_final: 0.6923 (t80) REVERT: B 395 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7428 (tp) REVERT: B 667 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7877 (t80) outliers start: 40 outliers final: 26 residues processed: 150 average time/residue: 0.2204 time to fit residues: 48.8424 Evaluate side-chains 137 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 0.0060 chunk 26 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 408 ASN ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11288 Z= 0.195 Angle : 0.630 12.691 15336 Z= 0.312 Chirality : 0.042 0.247 1758 Planarity : 0.004 0.038 2003 Dihedral : 4.948 56.554 1587 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.73 % Favored : 91.20 % Rotamer: Outliers : 3.44 % Allowed : 26.46 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1420 helix: 0.67 (0.21), residues: 702 sheet: -0.63 (0.58), residues: 89 loop : -2.26 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 658 HIS 0.013 0.001 HIS A 102 PHE 0.029 0.002 PHE A 241 TYR 0.011 0.001 TYR B 731 ARG 0.004 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.7445 (t0) cc_final: 0.7185 (t0) REVERT: A 241 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: A 328 ASP cc_start: 0.5927 (p0) cc_final: 0.5296 (t0) REVERT: A 448 ARG cc_start: 0.6079 (mmt90) cc_final: 0.5619 (tpt170) REVERT: B 158 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8516 (pp) REVERT: B 329 PHE cc_start: 0.7281 (t80) cc_final: 0.6959 (t80) REVERT: B 395 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7515 (tp) REVERT: B 667 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7775 (t80) outliers start: 39 outliers final: 31 residues processed: 145 average time/residue: 0.2160 time to fit residues: 46.2570 Evaluate side-chains 142 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.0000 chunk 127 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11288 Z= 0.236 Angle : 0.654 12.008 15336 Z= 0.323 Chirality : 0.043 0.223 1758 Planarity : 0.004 0.038 2003 Dihedral : 4.957 56.628 1587 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.08 % Favored : 90.85 % Rotamer: Outliers : 3.44 % Allowed : 26.72 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1420 helix: 0.74 (0.21), residues: 703 sheet: -0.57 (0.58), residues: 89 loop : -2.26 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 658 HIS 0.008 0.001 HIS A 595 PHE 0.028 0.002 PHE A 241 TYR 0.012 0.001 TYR A 214 ARG 0.005 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.7510 (t0) cc_final: 0.7269 (t0) REVERT: A 241 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: A 256 PHE cc_start: 0.7597 (m-80) cc_final: 0.7377 (m-80) REVERT: A 328 ASP cc_start: 0.5951 (p0) cc_final: 0.5413 (t0) REVERT: A 357 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: A 448 ARG cc_start: 0.5997 (mmt90) cc_final: 0.5600 (tpt170) REVERT: B 329 PHE cc_start: 0.7348 (t80) cc_final: 0.6977 (t80) REVERT: B 395 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7517 (tt) REVERT: B 667 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.6537 (m-80) outliers start: 39 outliers final: 32 residues processed: 139 average time/residue: 0.2170 time to fit residues: 45.0240 Evaluate side-chains 142 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 130 optimal weight: 0.0270 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 408 ASN A 621 HIS ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11288 Z= 0.195 Angle : 0.655 14.234 15336 Z= 0.319 Chirality : 0.042 0.212 1758 Planarity : 0.004 0.039 2003 Dihedral : 4.900 56.906 1587 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.87 % Favored : 91.06 % Rotamer: Outliers : 3.53 % Allowed : 26.98 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1420 helix: 0.76 (0.20), residues: 710 sheet: -0.69 (0.58), residues: 89 loop : -2.25 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 658 HIS 0.007 0.001 HIS A 595 PHE 0.028 0.002 PHE A 241 TYR 0.010 0.001 TYR B 731 ARG 0.005 0.000 ARG B 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 111 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.7417 (t0) cc_final: 0.7178 (t0) REVERT: A 241 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: A 328 ASP cc_start: 0.5908 (p0) cc_final: 0.5365 (t0) REVERT: A 357 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: A 448 ARG cc_start: 0.5994 (mmt90) cc_final: 0.5598 (tpt170) REVERT: B 329 PHE cc_start: 0.7328 (t80) cc_final: 0.7010 (t80) REVERT: B 395 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7496 (tt) REVERT: B 667 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.6469 (m-80) outliers start: 40 outliers final: 31 residues processed: 143 average time/residue: 0.2004 time to fit residues: 43.3534 Evaluate side-chains 142 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 20.0000 chunk 103 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.114651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088981 restraints weight = 31780.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.090834 restraints weight = 20123.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092008 restraints weight = 14835.664| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.201 Angle : 0.649 11.633 15336 Z= 0.317 Chirality : 0.043 0.421 1758 Planarity : 0.004 0.039 2003 Dihedral : 4.889 56.930 1587 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.94 % Favored : 90.99 % Rotamer: Outliers : 3.79 % Allowed : 26.72 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1420 helix: 0.76 (0.20), residues: 710 sheet: -0.73 (0.57), residues: 89 loop : -2.22 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 658 HIS 0.007 0.001 HIS A 595 PHE 0.028 0.002 PHE A 241 TYR 0.010 0.001 TYR B 731 ARG 0.004 0.000 ARG A 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.40 seconds wall clock time: 44 minutes 43.73 seconds (2683.73 seconds total)