Starting phenix.real_space_refine (version: dev) on Mon Dec 12 08:36:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwr_21945/12_2022/6wwr_21945_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwr_21945/12_2022/6wwr_21945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwr_21945/12_2022/6wwr_21945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwr_21945/12_2022/6wwr_21945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwr_21945/12_2022/6wwr_21945_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwr_21945/12_2022/6wwr_21945_updated.pdb" } resolution = 2.7 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 46": "OD1" <-> "OD2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "K GLU 407": "OE1" <-> "OE2" Residue "K GLU 426": "OE1" <-> "OE2" Residue "K ASP 468": "OD1" <-> "OD2" Residue "K GLU 498": "OE1" <-> "OE2" Residue "K PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 526": "OE1" <-> "OE2" Residue "K GLU 535": "OE1" <-> "OE2" Residue "K ARG 550": "NH1" <-> "NH2" Residue "K TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 579": "OD1" <-> "OD2" Residue "K ARG 644": "NH1" <-> "NH2" Residue "K ARG 683": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9719 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3458 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Conformer: "B" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} bond proxies already assigned to first conformer: 3510 Chain: "B" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3411 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain: "K" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2700 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 11, 'TRANS': 333} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 108 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 108 " occ=0.50 Time building chain proxies: 7.38, per 1000 atoms: 0.76 Number of scatterers: 9719 At special positions: 0 Unit cell: (108.075, 70.125, 113.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 7 15.00 Mg 1 11.99 O 1903 8.00 N 1654 7.00 C 6092 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: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 9 sheets defined 38.9% alpha, 15.2% 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 10 through 28 removed outlier: 4.204A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 41 removed outlier: 3.774A pdb=" N THR A 41 " --> pdb=" O SER A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 72 through 79 removed outlier: 4.107A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.684A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.054A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.867A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.654A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.562A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.711A pdb=" N LEU A 391 " --> pdb=" O TRP A 388 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 394 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.727A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.382A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.883A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.838A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.783A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.946A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 241 removed outlier: 3.532A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.743A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.822A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 387 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 405 through 425 removed outlier: 4.311A pdb=" N GLU B 410 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 424 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 456 through 459 No H-bonds generated for 'chain 'K' and resid 456 through 459' Processing helix chain 'K' and resid 464 through 472 removed outlier: 3.561A pdb=" N PHE K 471 " --> pdb=" O LEU K 467 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU K 472 " --> pdb=" O ASP K 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 491 No H-bonds generated for 'chain 'K' and resid 488 through 491' Processing helix chain 'K' and resid 501 through 516 removed outlier: 3.827A pdb=" N LYS K 515 " --> pdb=" O ALA K 511 " (cutoff:3.500A) Processing helix chain 'K' and resid 577 through 588 removed outlier: 4.497A pdb=" N GLN K 581 " --> pdb=" O SER K 578 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER K 582 " --> pdb=" O ASP K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 679 Processing helix chain 'K' and resid 692 through 696 Processing helix chain 'K' and resid 698 through 700 No H-bonds generated for 'chain 'K' and resid 698 through 700' Processing helix chain 'K' and resid 717 through 733 removed outlier: 4.104A pdb=" N ILE K 720 " --> pdb=" O ALA K 717 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU K 721 " --> pdb=" O SER K 718 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU K 724 " --> pdb=" O GLU K 721 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA K 730 " --> pdb=" O LEU K 727 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR K 731 " --> pdb=" O ARG K 728 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN K 732 " --> pdb=" O TYR K 729 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.896A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.525A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 351 through 356 removed outlier: 8.424A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 63 through 65 removed outlier: 8.516A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE B 202 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.959A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'K' and resid 440 through 443 removed outlier: 3.694A pdb=" N VAL K 398 " --> pdb=" O VAL K 440 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N THR K 395 " --> pdb=" O SER K 705 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR K 707 " --> pdb=" O THR K 395 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ALA K 397 " --> pdb=" O THR K 707 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET K 709 " --> pdb=" O ALA K 397 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ARG K 399 " --> pdb=" O MET K 709 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA K 711 " --> pdb=" O ARG K 399 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ARG K 401 " --> pdb=" O ALA K 711 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL K 713 " --> pdb=" O ARG K 401 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN K 475 " --> pdb=" O LYS K 706 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ALA K 708 " --> pdb=" O ASN K 475 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N CYS K 477 " --> pdb=" O ALA K 708 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE K 710 " --> pdb=" O CYS K 477 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE K 479 " --> pdb=" O ILE K 710 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR K 712 " --> pdb=" O PHE K 479 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N TYR K 481 " --> pdb=" O THR K 712 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N SER K 714 " --> pdb=" O TYR K 481 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE K 630 " --> pdb=" O GLN K 615 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL K 532 " --> pdb=" O HIS K 606 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU K 525 " --> pdb=" O VAL K 574 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL K 574 " --> pdb=" O LEU K 525 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 416 through 418 Processing sheet with id= H, first strand: chain 'K' and resid 530 through 533 Processing sheet with id= I, first strand: chain 'K' and resid 556 through 559 327 hydrogen bonds defined for protein. 813 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: 2.62 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1896 1.32 - 1.45: 2492 1.45 - 1.57: 5438 1.57 - 1.69: 11 1.69 - 1.81: 99 Bond restraints: 9936 Sorted by residual: bond pdb=" C27 TA1 B 502 " pdb=" O11 TA1 B 502 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C22 TA1 B 502 " pdb=" O09 TA1 B 502 " ideal model delta sigma weight residual 1.335 1.454 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C12 TA1 B 502 " pdb=" O04 TA1 B 502 " ideal model delta sigma weight residual 1.337 1.454 -0.117 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C03 TA1 B 502 " pdb=" O02 TA1 B 502 " ideal model delta sigma weight residual 1.333 1.442 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C10 TA1 B 502 " pdb=" C18 TA1 B 502 " ideal model delta sigma weight residual 1.611 1.521 0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 9931 not shown) Histogram of bond angle deviations from ideal: 88.08 - 97.66: 6 97.66 - 107.24: 393 107.24 - 116.82: 6523 116.82 - 126.39: 6437 126.39 - 135.97: 137 Bond angle restraints: 13496 Sorted by residual: angle pdb=" C PRO B 357 " pdb=" N PRO B 358 " pdb=" CA PRO B 358 " ideal model delta sigma weight residual 119.78 129.73 -9.95 1.03e+00 9.43e-01 9.33e+01 angle pdb=" C ARG B 276 " pdb=" N GLY B 277 " pdb=" CA GLY B 277 " ideal model delta sigma weight residual 120.34 127.76 -7.42 1.26e+00 6.30e-01 3.47e+01 angle pdb=" N GLU B 22 " pdb=" CA GLU B 22 " pdb=" C GLU B 22 " ideal model delta sigma weight residual 112.90 106.28 6.62 1.31e+00 5.83e-01 2.56e+01 angle pdb=" O GLY B 142 " pdb=" C GLY B 142 " pdb=" N THR B 143 " ideal model delta sigma weight residual 121.85 124.57 -2.72 5.60e-01 3.19e+00 2.35e+01 angle pdb=" CA SER B 275 " pdb=" C SER B 275 " pdb=" N ARG B 276 " ideal model delta sigma weight residual 115.27 121.46 -6.19 1.30e+00 5.92e-01 2.27e+01 ... (remaining 13491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 5789 33.80 - 67.60: 99 67.60 - 101.40: 6 101.40 - 135.20: 2 135.20 - 169.00: 2 Dihedral angle restraints: 5898 sinusoidal: 2367 harmonic: 3531 Sorted by residual: dihedral pdb=" CA GLU K 625 " pdb=" C GLU K 625 " pdb=" N HIS K 626 " pdb=" CA HIS K 626 " ideal model delta harmonic sigma weight residual -180.00 -134.03 -45.97 0 5.00e+00 4.00e-02 8.45e+01 dihedral pdb=" CA VAL K 621 " pdb=" C VAL K 621 " pdb=" N GLU K 622 " pdb=" CA GLU K 622 " ideal model delta harmonic sigma weight residual 180.00 137.25 42.75 0 5.00e+00 4.00e-02 7.31e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.73 -169.00 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 5895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1342 0.089 - 0.177: 128 0.177 - 0.266: 8 0.266 - 0.355: 1 0.355 - 0.444: 3 Chirality restraints: 1482 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.72 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ARG B 359 " pdb=" N ARG B 359 " pdb=" C ARG B 359 " pdb=" CB ARG B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA GLU B 22 " pdb=" N GLU B 22 " pdb=" C GLU B 22 " pdb=" CB GLU B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 1479 not shown) Planarity restraints: 1747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 358 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C PRO B 358 " -0.048 2.00e-02 2.50e+03 pdb=" O PRO B 358 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG B 359 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 226 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C ASN B 226 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN B 226 " 0.016 2.00e-02 2.50e+03 pdb=" N HIS B 227 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 TA1 B 502 " -0.027 2.00e-02 2.50e+03 2.13e-02 5.66e+00 pdb=" C30 TA1 B 502 " 0.008 2.00e-02 2.50e+03 pdb=" C31 TA1 B 502 " -0.020 2.00e-02 2.50e+03 pdb=" N01 TA1 B 502 " 0.032 2.00e-02 2.50e+03 pdb=" O14 TA1 B 502 " 0.007 2.00e-02 2.50e+03 ... (remaining 1744 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 76 2.55 - 3.14: 7660 3.14 - 3.73: 14645 3.73 - 4.31: 21372 4.31 - 4.90: 35966 Nonbonded interactions: 79719 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.967 2.170 nonbonded pdb=" OH TYR A 185 " pdb=" O MET A 398 " model vdw 2.051 2.440 nonbonded pdb=" O LEU B 192 " pdb=" OG1 THR B 196 " model vdw 2.065 2.440 nonbonded pdb=" OG SER B 25 " pdb=" OH TYR B 51 " model vdw 2.163 2.440 nonbonded pdb=" O LEU K 727 " pdb=" OG1 THR K 731 " model vdw 2.165 2.440 ... (remaining 79714 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6092 2.51 5 N 1654 2.21 5 O 1903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.460 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 29.620 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.123 9936 Z= 0.600 Angle : 0.962 11.008 13496 Z= 0.539 Chirality : 0.055 0.444 1482 Planarity : 0.006 0.052 1747 Dihedral : 14.629 168.998 3634 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.62 (0.21), residues: 1217 helix: -2.18 (0.20), residues: 479 sheet: -2.01 (0.32), residues: 212 loop : -2.65 (0.25), residues: 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 296 time to evaluate : 1.195 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 299 average time/residue: 1.0579 time to fit residues: 341.9210 Evaluate side-chains 234 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.0670 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 266 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 334 GLN B 424 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 9936 Z= 0.237 Angle : 0.621 8.173 13496 Z= 0.306 Chirality : 0.044 0.267 1482 Planarity : 0.005 0.039 1747 Dihedral : 10.116 166.870 1370 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.23 (0.23), residues: 1217 helix: -0.89 (0.23), residues: 480 sheet: -1.10 (0.34), residues: 215 loop : -2.13 (0.26), residues: 522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 1.174 Fit side-chains outliers start: 28 outliers final: 7 residues processed: 226 average time/residue: 1.1438 time to fit residues: 278.5106 Evaluate side-chains 194 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1535 time to fit residues: 2.3290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 206 ASN A 216 ASN A 233 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 342 GLN A 356 ASN A 372 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 279 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN K 534 ASN K 680 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 9936 Z= 0.326 Angle : 0.626 8.667 13496 Z= 0.309 Chirality : 0.046 0.246 1482 Planarity : 0.004 0.044 1747 Dihedral : 10.032 166.830 1370 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.75 (0.24), residues: 1217 helix: -0.57 (0.24), residues: 484 sheet: -0.67 (0.35), residues: 213 loop : -1.88 (0.27), residues: 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 1.084 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 234 average time/residue: 1.1860 time to fit residues: 297.8939 Evaluate side-chains 214 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.6928 time to fit residues: 4.6264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 0.0170 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 256 GLN B 165 ASN B 191 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 534 ASN K 680 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9936 Z= 0.282 Angle : 0.600 8.852 13496 Z= 0.293 Chirality : 0.045 0.237 1482 Planarity : 0.004 0.055 1747 Dihedral : 9.794 164.381 1370 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.35 (0.24), residues: 1217 helix: -0.34 (0.24), residues: 487 sheet: -0.20 (0.35), residues: 223 loop : -1.71 (0.28), residues: 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 225 average time/residue: 1.2582 time to fit residues: 302.9471 Evaluate side-chains 218 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 8 average time/residue: 0.7265 time to fit residues: 8.1930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 256 GLN B 6 HIS B 14 ASN B 256 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 534 ASN K 680 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9936 Z= 0.267 Angle : 0.597 8.739 13496 Z= 0.288 Chirality : 0.044 0.235 1482 Planarity : 0.004 0.060 1747 Dihedral : 9.661 162.830 1370 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.09 (0.24), residues: 1217 helix: -0.13 (0.24), residues: 488 sheet: 0.04 (0.35), residues: 230 loop : -1.62 (0.28), residues: 499 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 1.086 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 228 average time/residue: 1.1703 time to fit residues: 286.6910 Evaluate side-chains 223 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.5210 time to fit residues: 7.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 112 optimal weight: 0.0570 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 342 GLN A 372 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 534 ASN K 680 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9936 Z= 0.142 Angle : 0.544 7.638 13496 Z= 0.261 Chirality : 0.042 0.202 1482 Planarity : 0.004 0.049 1747 Dihedral : 9.234 157.892 1370 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 (0.25), residues: 1217 helix: 0.16 (0.25), residues: 487 sheet: 0.26 (0.35), residues: 233 loop : -1.49 (0.28), residues: 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 1.130 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 235 average time/residue: 1.2059 time to fit residues: 305.2602 Evaluate side-chains 217 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 4 average time/residue: 0.5282 time to fit residues: 4.0391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 116 optimal weight: 0.0040 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 301 GLN A 342 GLN A 372 GLN B 131 GLN B 298 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 427 HIS K 534 ASN K 680 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9936 Z= 0.212 Angle : 0.572 8.145 13496 Z= 0.276 Chirality : 0.043 0.216 1482 Planarity : 0.004 0.042 1747 Dihedral : 9.192 154.602 1370 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.56 (0.25), residues: 1217 helix: 0.19 (0.25), residues: 488 sheet: 0.52 (0.36), residues: 229 loop : -1.31 (0.28), residues: 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 1.266 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 228 average time/residue: 1.2419 time to fit residues: 303.6865 Evaluate side-chains 224 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.4574 time to fit residues: 4.7746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 301 GLN A 342 GLN A 372 GLN B 131 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 427 HIS K 534 ASN K 680 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9936 Z= 0.274 Angle : 0.600 7.885 13496 Z= 0.290 Chirality : 0.045 0.232 1482 Planarity : 0.004 0.055 1747 Dihedral : 9.266 155.498 1370 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.49 (0.25), residues: 1217 helix: 0.23 (0.25), residues: 486 sheet: 0.62 (0.36), residues: 229 loop : -1.28 (0.28), residues: 502 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 1.186 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 224 average time/residue: 1.2519 time to fit residues: 300.3419 Evaluate side-chains 230 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.1311 time to fit residues: 2.8225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 47 optimal weight: 0.0570 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 301 GLN B 131 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 534 ASN K 680 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9936 Z= 0.178 Angle : 0.570 7.215 13496 Z= 0.275 Chirality : 0.043 0.213 1482 Planarity : 0.004 0.042 1747 Dihedral : 9.023 151.777 1370 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.38 (0.25), residues: 1217 helix: 0.36 (0.25), residues: 486 sheet: 0.68 (0.36), residues: 231 loop : -1.29 (0.28), residues: 500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 1.054 Fit side-chains outliers start: 20 outliers final: 17 residues processed: 227 average time/residue: 1.2822 time to fit residues: 311.5394 Evaluate side-chains 218 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.1118 time to fit residues: 1.9584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 285 GLN A 301 GLN A 342 GLN A 372 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 534 ASN K 680 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9936 Z= 0.227 Angle : 0.584 7.467 13496 Z= 0.284 Chirality : 0.044 0.225 1482 Planarity : 0.004 0.041 1747 Dihedral : 9.014 150.243 1370 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.39 (0.25), residues: 1217 helix: 0.37 (0.25), residues: 488 sheet: 0.67 (0.36), residues: 231 loop : -1.30 (0.28), residues: 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 1.189 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 221 average time/residue: 1.2517 time to fit residues: 298.5430 Evaluate side-chains 216 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 1.5295 time to fit residues: 4.8667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 301 GLN A 342 GLN A 372 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 427 HIS K 534 ASN K 680 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.125274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104047 restraints weight = 21045.611| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.51 r_work: 0.3278 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 9936 Z= 0.306 Angle : 0.610 7.621 13496 Z= 0.297 Chirality : 0.045 0.239 1482 Planarity : 0.004 0.041 1747 Dihedral : 9.209 153.698 1370 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.46 (0.25), residues: 1217 helix: 0.27 (0.25), residues: 490 sheet: 0.60 (0.36), residues: 232 loop : -1.29 (0.28), residues: 495 =============================================================================== Job complete usr+sys time: 5022.38 seconds wall clock time: 89 minutes 19.08 seconds (5359.08 seconds total)