Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 23:30:59 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/01_2021/7jpp_22418_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/01_2021/7jpp_22418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/01_2021/7jpp_22418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/01_2021/7jpp_22418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/01_2021/7jpp_22418_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpp_22418/01_2021/7jpp_22418_updated.pdb" } resolution = 3.7 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= 0.003 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 14872 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2515 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Chain: "C" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4886 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 24, 'TRANS': 572} Chain breaks: 7 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3312 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 19, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.98, per 1000 atoms: 0.54 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 14872 At special positions: 0 Unit cell: (93.09, 119.84, 154.08, 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 69 16.00 P 6 15.00 Mg 2 11.99 O 2732 8.00 N 2516 7.00 C 9547 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 Amimo 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: 6.39 Conformation dependent library (CDL) restraints added in 2.2 seconds 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 5 sheets defined 54.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 762 through 768 Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 795 through 809 removed outlier: 3.664A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 828 removed outlier: 3.602A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 284 through 306 removed outlier: 3.937A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N HIS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.717A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 486 through 502 removed outlier: 3.713A pdb=" N LEU B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 37 through 86 removed outlier: 4.034A pdb=" N PHE C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 128 removed outlier: 4.417A pdb=" N PHE C 118 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 Processing helix chain 'C' and resid 181 through 191 Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.732A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.961A pdb=" N LEU C 262 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.521A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 270' Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.563A pdb=" N PHE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 338 Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.714A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 370 through 377 removed outlier: 3.712A pdb=" N GLU C 377 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.816A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.513A pdb=" N GLU C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.616A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 481 Processing helix chain 'C' and resid 488 through 500 Processing helix chain 'C' and resid 550 through 567 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 585 through 592 Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.859A pdb=" N LEU C 600 " --> pdb=" O PRO C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 637 Processing helix chain 'C' and resid 646 through 660 Processing helix chain 'C' and resid 676 through 689 Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 41 through 56 Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.842A pdb=" N LYS D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.813A pdb=" N ILE D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 313 through 320 removed outlier: 3.567A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 369 through 381 Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 69 through 84 Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 127 through 130 Processing helix chain 'E' and resid 135 through 142 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 184 through 193 removed outlier: 4.401A pdb=" N HIS E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 233 through 242 Proline residue: E 239 - end of helix Processing helix chain 'E' and resid 250 through 266 Proline residue: E 259 - end of helix removed outlier: 4.010A pdb=" N LYS E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 304 through 317 removed outlier: 3.811A pdb=" N LEU E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 359 through 369 Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.979A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 422 Processing helix chain 'E' and resid 427 through 431 Processing sheet with id= A, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.558A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 311 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 388 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE B 421 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 390 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N SER B 423 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE B 392 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 335 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU B 391 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 337 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 271 through 277 removed outlier: 6.402A pdb=" N ILE C 100 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU C 274 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 102 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE C 276 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA C 104 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 214 through 216 removed outlier: 8.103A pdb=" N ILE D 215 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 64 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL D 154 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= E, first strand: chain 'E' and resid 175 through 179 removed outlier: 3.708A pdb=" N PHE E 175 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLY E 37 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER E 158 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4256 1.34 - 1.46: 2834 1.46 - 1.58: 7980 1.58 - 1.70: 10 1.70 - 1.82: 104 Bond restraints: 15184 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C5 ATP E 501 " pdb=" N7 ATP E 501 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 15179 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.64: 259 105.64 - 113.15: 8133 113.15 - 120.66: 7163 120.66 - 128.17: 4872 128.17 - 135.68: 125 Bond angle restraints: 20552 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 117.99 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 118.19 18.64 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 123.89 15.98 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 123.79 13.04 1.00e+00 1.00e+00 1.70e+02 angle pdb=" C5 ATP E 501 " pdb=" C4 ATP E 501 " pdb=" N3 ATP E 501 " ideal model delta sigma weight residual 126.80 118.19 8.61 1.00e+00 1.00e+00 7.41e+01 ... (remaining 20547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 8177 17.63 - 35.26: 791 35.26 - 52.88: 144 52.88 - 70.51: 37 70.51 - 88.14: 24 Dihedral angle restraints: 9173 sinusoidal: 3779 harmonic: 5394 Sorted by residual: dihedral pdb=" CA THR C 130 " pdb=" C THR C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS D 34 " pdb=" C HIS D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN D 358 " pdb=" C GLN D 358 " pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2009 0.088 - 0.176: 303 0.176 - 0.264: 28 0.264 - 0.352: 2 0.352 - 0.441: 2 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CB ILE C 435 " pdb=" CA ILE C 435 " pdb=" CG1 ILE C 435 " pdb=" CG2 ILE C 435 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA LEU A 832 " pdb=" N LEU A 832 " pdb=" C LEU A 832 " pdb=" CB LEU A 832 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2341 not shown) Planarity restraints: 2591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 238 " 0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO E 239 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 239 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 239 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 44 " -0.007 2.00e-02 2.50e+03 2.23e-02 9.93e+00 pdb=" CG TYR D 44 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 44 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 44 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR D 44 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 44 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 44 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 44 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 122 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C THR C 122 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 122 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU C 123 " -0.018 2.00e-02 2.50e+03 ... (remaining 2588 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 84 2.63 - 3.20: 12674 3.20 - 3.76: 22799 3.76 - 4.33: 30546 4.33 - 4.90: 49643 Nonbonded interactions: 115746 Sorted by model distance: nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.061 2.230 nonbonded pdb=" O1G ATP D 901 " pdb="MG MG D 902 " model vdw 2.148 2.230 nonbonded pdb=" OH TYR D 44 " pdb=" OE1 GLU D 83 " model vdw 2.235 2.440 nonbonded pdb=" O1A ATP E 501 " pdb="MG MG E 502 " model vdw 2.280 2.230 nonbonded pdb=" O LEU C 419 " pdb=" OG1 THR C 423 " model vdw 2.297 2.440 ... (remaining 115741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 14872 True True 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 6 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9547 2.51 5 N 2516 2.21 5 O 2732 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables 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: 1.300 Set model interpretation parameters: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.840 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.080 Process input model: 43.580 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.460 Internal consistency checks: 0.000 Total: 56.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.007 0.080 15184 Angle : 1.181 21.883 20552 Chirality : 0.064 0.441 2344 Planarity : 0.007 0.094 2591 Dihedral : 15.252 88.139 5645 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 0.00 % 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: -1.90 (0.17), residues: 1786 helix: -0.84 (0.14), residues: 1054 sheet: -0.61 (0.41), residues: 131 loop : -1.96 (0.22), residues: 601 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.930 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.3011 time to fit residues: 95.6661 Evaluate side-chains 165 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 0.0670 chunk 162 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 398 GLN B 411 GLN B 487 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 87 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN ** C 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 75 GLN E 256 ASN E 350 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.051 15184 Angle : 0.496 7.375 20552 Chirality : 0.037 0.138 2344 Planarity : 0.004 0.065 2591 Dihedral : 4.799 83.416 1955 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 1786 helix: 0.43 (0.15), residues: 1071 sheet: 0.25 (0.47), residues: 114 loop : -1.78 (0.22), residues: 601 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 242 time to evaluate : 2.041 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.2980 time to fit residues: 75.3740 Evaluate side-chains 160 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.0270 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 362 HIS B 394 ASN B 503 GLN B 563 ASN C 128 ASN ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN C 637 HIS D 358 GLN E 256 ASN E 282 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.050 15184 Angle : 0.512 6.590 20552 Chirality : 0.039 0.140 2344 Planarity : 0.004 0.089 2591 Dihedral : 4.705 81.969 1955 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1786 helix: 0.98 (0.16), residues: 1053 sheet: 0.07 (0.44), residues: 133 loop : -1.71 (0.22), residues: 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 217 time to evaluate : 2.009 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.2983 time to fit residues: 68.4460 Evaluate side-chains 155 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 173 optimal weight: 0.3980 chunk 85 optimal weight: 0.3980 chunk 154 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 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 769 ASN B 411 GLN B 468 GLN B 563 ASN C 110 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN D 334 HIS D 410 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.068 15184 Angle : 0.495 6.177 20552 Chirality : 0.038 0.154 2344 Planarity : 0.004 0.098 2591 Dihedral : 4.567 74.229 1955 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1786 helix: 1.17 (0.16), residues: 1057 sheet: 0.46 (0.47), residues: 124 loop : -1.77 (0.23), residues: 605 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 214 time to evaluate : 2.156 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.3126 time to fit residues: 70.4340 Evaluate side-chains 146 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 147 optimal weight: 0.0030 chunk 119 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS B 435 HIS C 339 GLN C 379 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN E 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.079 15184 Angle : 0.514 7.839 20552 Chirality : 0.039 0.150 2344 Planarity : 0.004 0.088 2591 Dihedral : 4.518 55.989 1955 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1786 helix: 1.18 (0.16), residues: 1062 sheet: 0.23 (0.45), residues: 139 loop : -1.73 (0.23), residues: 585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.935 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2902 time to fit residues: 61.8463 Evaluate side-chains 143 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.096 15184 Angle : 0.471 6.404 20552 Chirality : 0.038 0.142 2344 Planarity : 0.004 0.097 2591 Dihedral : 4.210 56.175 1955 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.00 % 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: 0.43 (0.20), residues: 1786 helix: 1.34 (0.16), residues: 1065 sheet: 0.21 (0.44), residues: 148 loop : -1.72 (0.23), residues: 573 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.972 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2876 time to fit residues: 62.9105 Evaluate side-chains 148 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS E 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.108 15184 Angle : 0.477 7.256 20552 Chirality : 0.037 0.148 2344 Planarity : 0.004 0.112 2591 Dihedral : 4.052 56.509 1955 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.00 % 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: 0.57 (0.20), residues: 1786 helix: 1.45 (0.16), residues: 1068 sheet: 0.16 (0.42), residues: 160 loop : -1.68 (0.24), residues: 558 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.877 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2995 time to fit residues: 60.7322 Evaluate side-chains 142 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.122 15184 Angle : 0.479 8.974 20552 Chirality : 0.037 0.138 2344 Planarity : 0.004 0.114 2591 Dihedral : 3.979 56.423 1955 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.00 % 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: 0.66 (0.20), residues: 1786 helix: 1.50 (0.16), residues: 1068 sheet: 0.26 (0.42), residues: 160 loop : -1.63 (0.24), residues: 558 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2804 time to fit residues: 58.7079 Evaluate side-chains 152 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 96 optimal weight: 0.0170 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN B 411 GLN B 416 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.138 15184 Angle : 0.483 11.311 20552 Chirality : 0.037 0.139 2344 Planarity : 0.004 0.122 2591 Dihedral : 3.941 56.430 1955 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.00 % 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: 0.73 (0.20), residues: 1786 helix: 1.56 (0.16), residues: 1068 sheet: 0.30 (0.42), residues: 160 loop : -1.62 (0.24), residues: 558 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.828 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2776 time to fit residues: 55.7499 Evaluate side-chains 148 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 164 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 109 optimal weight: 0.0470 chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.159 15184 Angle : 0.487 14.829 20552 Chirality : 0.037 0.139 2344 Planarity : 0.004 0.138 2591 Dihedral : 3.882 56.677 1955 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.00 % 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: 0.76 (0.20), residues: 1786 helix: 1.57 (0.16), residues: 1071 sheet: 0.36 (0.43), residues: 162 loop : -1.61 (0.24), residues: 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield and 0 Emsley and 1786 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.804 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2724 time to fit residues: 56.2229 Evaluate side-chains 151 residues out of total 1678 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 0.0980 chunk 142 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 HIS C 406 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125125 restraints weight = 25504.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127573 restraints weight = 16265.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129079 restraints weight = 12014.408| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.003 0.159 15184 ANGLE : 0.486 15.639 20552 CHIRALITY : 0.037 0.140 2344 PLANARITY : 0.004 0.145 2591 DIHEDRAL : 3.864 56.560 1955 MIN NONBONDED DISTANCE : 2.040 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 6.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.02 % FAVORED : 97.98 % ROTAMER OUTLIERS : 0.00 % 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: 0.79 (0.20), RESIDUES: 1786 HELIX: 1.59 (0.17), RESIDUES: 1071 SHEET: 0.40 (0.43), RESIDUES: 162 LOOP : -1.59 (0.25), RESIDUES: 553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.159 15184 Angle : 0.486 15.639 20552 Chirality : 0.037 0.140 2344 Planarity : 0.004 0.145 2591 Dihedral : 3.864 56.560 1955 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.00 % 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: 0.79 (0.20), residues: 1786 helix: 1.59 (0.17), residues: 1071 sheet: 0.40 (0.43), residues: 162 loop : -1.59 (0.25), residues: 553 =============================================================================== Job complete usr+sys time: 2662.11 seconds wall clock time: 50 minutes 2.23 seconds (3002.23 seconds total)