Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 01:11:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/04_2023/6m5s_30091.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/04_2023/6m5s_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_30091/04_2023/6m5s_30091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/04_2023/6m5s_30091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/04_2023/6m5s_30091.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5s_30091/04_2023/6m5s_30091.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.87, per 1000 atoms: 0.53 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: 4.06 Conformation dependent library (CDL) restraints added in 1.6 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: 0.56 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: 3.19 Time building geometry restraints manager: 4.42 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: 3.520 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: 10.780 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 31.160 Find NCS groups from input model: 0.370 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.930 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.350 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 outliers start: 60 outliers final: 10 residues processed: 334 average time/residue: 0.2964 time to fit residues: 131.0897 Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1021 time to fit residues: 3.5887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 82 optimal weight: 0.0270 chunk 128 optimal weight: 8.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- 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 A 102 HIS A 133 GLN A 135 ASN A 155 GLN A 211 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 53 GLN B 124 HIS B 152 GLN ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 HIS B 621 GLN C 103 HIS C 126 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2925 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= 0.194 Angle : 0.687 10.588 15336 Z= 0.342 Chirality : 0.043 0.324 1758 Planarity : 0.005 0.040 2003 Dihedral : 4.943 26.260 1582 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.70 % Rotamer Outliers : 3.88 % 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: -2.61 (0.21), residues: 1420 helix: -0.73 (0.19), residues: 691 sheet: -1.25 (0.52), residues: 86 loop : -2.99 (0.23), residues: 643 *********************** 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 203 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 159 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 18 residues processed: 194 average time/residue: 0.2662 time to fit residues: 71.6962 Evaluate side-chains 130 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1118 time to fit residues: 5.5475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 359 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 210 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 11288 Z= 0.342 Angle : 0.734 11.718 15336 Z= 0.375 Chirality : 0.045 0.322 1758 Planarity : 0.006 0.080 2003 Dihedral : 5.046 27.528 1582 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.70 % Rotamer Outliers : 3.70 % 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: -2.14 (0.22), residues: 1420 helix: -0.43 (0.20), residues: 701 sheet: -1.18 (0.49), residues: 114 loop : -2.69 (0.26), residues: 605 *********************** 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 163 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 155 average time/residue: 0.2160 time to fit residues: 49.7298 Evaluate side-chains 130 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1069 time to fit residues: 6.3857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 114 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 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** B 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11288 Z= 0.195 Angle : 0.637 11.949 15336 Z= 0.317 Chirality : 0.041 0.210 1758 Planarity : 0.004 0.049 2003 Dihedral : 4.756 27.139 1582 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.55 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.23), residues: 1420 helix: 0.07 (0.20), residues: 696 sheet: -1.12 (0.49), residues: 114 loop : -2.54 (0.26), residues: 610 *********************** 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 151 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 145 average time/residue: 0.2431 time to fit residues: 53.1249 Evaluate side-chains 121 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1783 time to fit residues: 3.9786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 117 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 chunk 123 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 overall best weight: 3.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11288 Z= 0.261 Angle : 0.663 10.862 15336 Z= 0.332 Chirality : 0.042 0.159 1758 Planarity : 0.004 0.037 2003 Dihedral : 4.693 25.245 1582 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.73 % Favored : 91.20 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1420 helix: 0.24 (0.20), residues: 695 sheet: -0.78 (0.55), residues: 97 loop : -2.41 (0.26), residues: 628 *********************** 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 147 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 140 average time/residue: 0.2086 time to fit residues: 44.6483 Evaluate side-chains 122 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1101 time to fit residues: 5.5076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 11288 Z= 0.308 Angle : 0.681 12.647 15336 Z= 0.344 Chirality : 0.043 0.170 1758 Planarity : 0.005 0.039 2003 Dihedral : 4.799 26.059 1582 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.72 % Favored : 90.21 % Rotamer Outliers : 2.20 % 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: -1.33 (0.23), residues: 1420 helix: 0.31 (0.20), residues: 705 sheet: -0.79 (0.55), residues: 89 loop : -2.36 (0.25), residues: 626 *********************** 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 142 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 7 residues processed: 136 average time/residue: 0.2188 time to fit residues: 44.2662 Evaluate side-chains 117 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1131 time to fit residues: 3.1202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 100 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 136 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 HIS ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11288 Z= 0.179 Angle : 0.633 10.759 15336 Z= 0.314 Chirality : 0.041 0.207 1758 Planarity : 0.004 0.035 2003 Dihedral : 4.547 26.516 1582 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer Outliers : 0.88 % 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: -1.03 (0.23), residues: 1420 helix: 0.59 (0.20), residues: 711 sheet: -0.65 (0.56), residues: 89 loop : -2.28 (0.26), residues: 620 *********************** 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 136 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 131 average time/residue: 0.2343 time to fit residues: 44.9058 Evaluate side-chains 117 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1056 time to fit residues: 2.9106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5498 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= 0.210 Angle : 0.637 10.460 15336 Z= 0.315 Chirality : 0.042 0.198 1758 Planarity : 0.004 0.037 2003 Dihedral : 4.493 26.923 1582 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer Outliers : 0.71 % 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: -0.95 (0.23), residues: 1420 helix: 0.68 (0.20), residues: 711 sheet: -0.65 (0.57), residues: 89 loop : -2.26 (0.26), residues: 620 *********************** 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 122 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 117 average time/residue: 0.2292 time to fit residues: 40.0644 Evaluate side-chains 111 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1045 time to fit residues: 2.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 100 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11288 Z= 0.182 Angle : 0.639 13.438 15336 Z= 0.313 Chirality : 0.042 0.182 1758 Planarity : 0.004 0.034 2003 Dihedral : 4.401 26.121 1582 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer Outliers : 0.62 % 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: -0.85 (0.23), residues: 1420 helix: 0.81 (0.20), residues: 703 sheet: -0.66 (0.57), residues: 89 loop : -2.23 (0.25), residues: 628 *********************** 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 122 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 119 average time/residue: 0.2256 time to fit residues: 40.1230 Evaluate side-chains 110 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1112 time to fit residues: 2.3212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0040 chunk 63 optimal weight: 0.2980 chunk 93 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11288 Z= 0.187 Angle : 0.638 11.283 15336 Z= 0.314 Chirality : 0.042 0.177 1758 Planarity : 0.004 0.034 2003 Dihedral : 4.359 25.501 1582 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1420 helix: 0.90 (0.20), residues: 702 sheet: -0.64 (0.57), residues: 89 loop : -2.17 (0.25), residues: 629 ********************** 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 116 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 116 average time/residue: 0.2314 time to fit residues: 40.1604 Evaluate side-chains 104 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1108 time to fit residues: 2.2611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 40.0000 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.115002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.089326 restraints weight = 31475.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091205 restraints weight = 19989.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092458 restraints weight = 14680.839| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5834 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= 0.197 Angle : 0.638 10.361 15336 Z= 0.313 Chirality : 0.042 0.170 1758 Planarity : 0.004 0.034 2003 Dihedral : 4.332 25.269 1582 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer Outliers : 0.62 % 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: -0.73 (0.23), residues: 1420 helix: 0.91 (0.20), residues: 699 sheet: -0.70 (0.57), residues: 89 loop : -2.15 (0.25), residues: 632 =============================================================================== Job complete usr+sys time: 2100.50 seconds wall clock time: 39 minutes 18.70 seconds (2358.70 seconds total)