Starting phenix.real_space_refine (version: dev) on Mon Apr 4 23:36:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wws_21946/04_2022/6wws_21946_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wws_21946/04_2022/6wws_21946.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/6wws_21946/04_2022/6wws_21946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wws_21946/04_2022/6wws_21946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wws_21946/04_2022/6wws_21946_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wws_21946/04_2022/6wws_21946_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 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9696 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: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 19, 'TRANS': 408, 'PCIS': 1} Chain: "K" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2708 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 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: 7.46, per 1000 atoms: 0.77 Number of scatterers: 9696 At special positions: 0 Unit cell: (108.672, 76.41, 112.068, 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 8 15.00 Mg 1 11.99 O 1896 8.00 N 1650 7.00 C 6079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 9 sheets defined 38.5% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.782A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.413A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.679A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.758A 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 243 removed outlier: 4.350A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.263A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (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 294 removed outlier: 3.679A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' 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 removed outlier: 3.513A pdb=" N ALA A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.988A pdb=" N TRP A 388 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 389 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 391 " --> pdb=" O TRP A 388 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 394 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.987A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.678A pdb=" N MET A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.578A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (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 71 through 77 removed outlier: 3.538A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) 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 101 through 105 Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.690A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.681A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.849A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 4.120A 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 236 removed outlier: 3.765A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 278 through 281 Processing helix chain 'B' and resid 286 through 293 removed outlier: 3.697A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) 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: 3.800A 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 372 through 389 removed outlier: 4.085A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.588A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.841A pdb=" N THR B 409 " --> pdb=" O MET B 406 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU B 410 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN B 414 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET B 415 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 420 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN B 424 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 408 No H-bonds generated for 'chain 'K' and resid 405 through 408' Processing helix chain 'K' and resid 455 through 461 removed outlier: 3.566A pdb=" N GLU K 460 " --> pdb=" O THR K 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 470 removed outlier: 3.661A pdb=" N ARG K 469 " --> pdb=" O PRO K 465 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 501 through 513 removed outlier: 3.702A pdb=" N ASP K 508 " --> pdb=" O ARG K 504 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN K 512 " --> pdb=" O ASP K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 577 through 587 Processing helix chain 'K' and resid 653 through 680 removed outlier: 3.508A pdb=" N SER K 676 " --> pdb=" O ILE K 672 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU K 677 " --> pdb=" O SER K 673 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN K 678 " --> pdb=" O ALA K 674 " (cutoff:3.500A) 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 721 through 733 removed outlier: 3.521A pdb=" N GLN K 732 " --> pdb=" O ARG K 728 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA K 733 " --> pdb=" O TYR K 729 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.416A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 352 through 356 removed outlier: 6.874A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.746A 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 66 removed outlier: 8.582A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLY B 132 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE B 7 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN B 134 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA B 9 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR B 136 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (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 'B' and resid 269 through 271 removed outlier: 3.875A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 440 through 443 removed outlier: 4.067A pdb=" N GLN K 393 " --> pdb=" O SER K 705 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN K 475 " --> pdb=" O LYS K 706 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ALA K 708 " --> pdb=" O ASN K 475 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS K 477 " --> pdb=" O ALA K 708 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE K 710 " --> pdb=" O CYS K 477 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE K 479 " --> pdb=" O ILE K 710 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR K 712 " --> pdb=" O PHE K 479 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR K 481 " --> pdb=" O THR K 712 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE K 630 " --> pdb=" O GLN K 615 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR K 616 " --> pdb=" O SER K 522 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 416 through 418 Processing sheet with id= I, first strand: chain 'K' and resid 555 through 558 removed outlier: 4.268A pdb=" N ARG K 555 " --> pdb=" O GLU K 567 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 783 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: 2.81 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1648 1.31 - 1.43: 2650 1.43 - 1.56: 5502 1.56 - 1.69: 13 1.69 - 1.81: 100 Bond restraints: 9913 Sorted by residual: bond pdb=" O3A ANP K 801 " pdb=" PB ANP K 801 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C22 TA1 B 502 " pdb=" O09 TA1 B 502 " ideal model delta sigma weight residual 1.335 1.458 -0.123 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C27 TA1 B 502 " pdb=" O11 TA1 B 502 " ideal model delta sigma weight residual 1.329 1.447 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C03 TA1 B 502 " pdb=" O02 TA1 B 502 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C12 TA1 B 502 " pdb=" O04 TA1 B 502 " ideal model delta sigma weight residual 1.337 1.443 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 9908 not shown) Histogram of bond angle deviations from ideal: 87.72 - 97.84: 5 97.84 - 107.95: 543 107.95 - 118.07: 6981 118.07 - 128.18: 5832 128.18 - 138.30: 106 Bond angle restraints: 13467 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 119.90 130.36 -10.46 1.02e+00 9.61e-01 1.05e+02 angle pdb=" C LEU B 228 " pdb=" N VAL B 229 " pdb=" CA VAL B 229 " ideal model delta sigma weight residual 120.42 131.74 -11.32 1.42e+00 4.96e-01 6.36e+01 angle pdb=" CA THR A 179 " pdb=" C THR A 179 " pdb=" O THR A 179 " ideal model delta sigma weight residual 120.53 112.21 8.32 1.18e+00 7.18e-01 4.97e+01 angle pdb=" C LEU K 675 " pdb=" N SER K 676 " pdb=" CA SER K 676 " ideal model delta sigma weight residual 120.29 129.35 -9.06 1.42e+00 4.96e-01 4.07e+01 angle pdb=" C TYR A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta sigma weight residual 119.76 125.86 -6.10 1.00e+00 1.00e+00 3.72e+01 ... (remaining 13462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 5709 34.26 - 68.53: 150 68.53 - 102.79: 12 102.79 - 137.05: 2 137.05 - 171.32: 2 Dihedral angle restraints: 5875 sinusoidal: 2354 harmonic: 3521 Sorted by residual: dihedral pdb=" CD ARG K 728 " pdb=" NE ARG K 728 " pdb=" CZ ARG K 728 " pdb=" NH1 ARG K 728 " ideal model delta sinusoidal sigma weight residual 0.00 -71.29 71.29 1 1.00e+01 1.00e-02 6.52e+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 -119.41 -171.32 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" CD ARG A 422 " pdb=" NE ARG A 422 " pdb=" CZ ARG A 422 " pdb=" NH1 ARG A 422 " ideal model delta sinusoidal sigma weight residual 0.00 59.11 -59.11 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 5872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1311 0.103 - 0.205: 127 0.205 - 0.308: 32 0.308 - 0.411: 6 0.411 - 0.514: 4 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA GLU A 113 " pdb=" N GLU A 113 " pdb=" C GLU A 113 " pdb=" CB GLU A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 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 -2.73 -0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CA THR B 72 " pdb=" N THR B 72 " pdb=" C THR B 72 " pdb=" CB THR B 72 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 1477 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 728 " -1.037 9.50e-02 1.11e+02 4.65e-01 1.30e+02 pdb=" NE ARG K 728 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG K 728 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 728 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG K 728 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 422 " -0.897 9.50e-02 1.11e+02 4.02e-01 9.89e+01 pdb=" NE ARG A 422 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 422 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 422 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 422 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 67 " -0.050 2.00e-02 2.50e+03 9.94e-02 9.87e+01 pdb=" C ASP B 67 " 0.172 2.00e-02 2.50e+03 pdb=" O ASP B 67 " -0.066 2.00e-02 2.50e+03 pdb=" N LEU B 68 " -0.056 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 183 2.64 - 3.21: 8519 3.21 - 3.77: 14386 3.77 - 4.34: 21386 4.34 - 4.90: 34982 Nonbonded interactions: 79456 Sorted by model distance: nonbonded pdb=" O SER B 275 " pdb=" OG SER B 275 " model vdw 2.077 2.440 nonbonded pdb=" OG1 THR A 271 " pdb=" O ASN A 300 " model vdw 2.125 2.440 nonbonded pdb=" O PRO A 222 " pdb=" OG SER B 322 " model vdw 2.129 2.440 nonbonded pdb=" OH TYR A 172 " pdb=" CD1 LEU A 391 " model vdw 2.149 3.460 nonbonded pdb=" OE1 GLU B 3 " pdb=" NH2 ARG B 62 " model vdw 2.183 2.520 ... (remaining 79451 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 8 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6079 2.51 5 N 1650 2.21 5 O 1896 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: 2.680 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: 0.000 Extract box with map and model: 14.550 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 30.990 Find NCS groups from input model: 0.310 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:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.010 0.146 9913 Z= 0.631 Angle : 1.279 16.842 13467 Z= 0.795 Chirality : 0.073 0.514 1480 Planarity : 0.018 0.465 1740 Dihedral : 15.941 171.316 3617 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.53 % Favored : 93.14 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.71 % 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: -3.99 (0.20), residues: 1213 helix: -2.74 (0.19), residues: 448 sheet: -1.44 (0.35), residues: 210 loop : -3.02 (0.21), residues: 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 293 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 8 residues processed: 314 average time/residue: 1.0617 time to fit residues: 360.5236 Evaluate side-chains 225 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.6203 time to fit residues: 3.6695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 36 optimal weight: 0.0370 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 107 HIS A 133 GLN B 8 GLN B 43 GLN B 375 GLN K 615 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 9913 Z= 0.222 Angle : 0.581 7.795 13467 Z= 0.290 Chirality : 0.044 0.190 1480 Planarity : 0.005 0.052 1740 Dihedral : 9.851 177.335 1359 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 3.54 % 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: -2.64 (0.22), residues: 1213 helix: -1.45 (0.23), residues: 457 sheet: -0.75 (0.34), residues: 235 loop : -2.45 (0.24), residues: 521 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 226 time to evaluate : 1.112 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 14 residues processed: 251 average time/residue: 1.0145 time to fit residues: 276.5412 Evaluate side-chains 218 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.1583 time to fit residues: 2.5105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 57 ASN B 190 HIS K 534 ASN K 588 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 9913 Z= 0.349 Angle : 0.610 7.802 13467 Z= 0.300 Chirality : 0.046 0.196 1480 Planarity : 0.005 0.063 1740 Dihedral : 9.621 174.585 1359 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 3.35 % 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: -2.03 (0.23), residues: 1213 helix: -0.83 (0.25), residues: 453 sheet: -0.28 (0.35), residues: 224 loop : -2.26 (0.23), residues: 536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 226 time to evaluate : 2.059 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 248 average time/residue: 1.0586 time to fit residues: 285.3001 Evaluate side-chains 236 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 5 average time/residue: 0.3425 time to fit residues: 3.6873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 56 optimal weight: 0.0870 chunk 12 optimal weight: 0.2980 chunk 52 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 GLN A 206 ASN A 356 ASN B 347 ASN B 348 ASN K 732 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 9913 Z= 0.185 Angle : 0.533 6.843 13467 Z= 0.261 Chirality : 0.042 0.175 1480 Planarity : 0.004 0.039 1740 Dihedral : 9.193 169.855 1359 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 3.35 % 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: -1.52 (0.24), residues: 1213 helix: -0.42 (0.25), residues: 457 sheet: -0.02 (0.36), residues: 225 loop : -1.95 (0.24), residues: 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 1.112 Fit side-chains outliers start: 34 outliers final: 22 residues processed: 234 average time/residue: 1.0152 time to fit residues: 258.8903 Evaluate side-chains 224 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 7 average time/residue: 0.1638 time to fit residues: 3.3191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 GLN A 356 ASN A 380 ASN B 52 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9913 Z= 0.278 Angle : 0.552 6.647 13467 Z= 0.271 Chirality : 0.044 0.203 1480 Planarity : 0.004 0.038 1740 Dihedral : 9.136 168.190 1359 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 3.44 % 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: -1.14 (0.24), residues: 1213 helix: -0.08 (0.26), residues: 449 sheet: 0.25 (0.37), residues: 222 loop : -1.77 (0.24), residues: 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 1.112 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 234 average time/residue: 1.0345 time to fit residues: 262.7120 Evaluate side-chains 222 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 7 average time/residue: 0.1437 time to fit residues: 3.0981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.3980 chunk 104 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 GLN A 356 ASN A 380 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9913 Z= 0.182 Angle : 0.516 6.640 13467 Z= 0.251 Chirality : 0.042 0.173 1480 Planarity : 0.004 0.035 1740 Dihedral : 8.851 163.803 1359 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 3.35 % 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: -1.00 (0.24), residues: 1213 helix: 0.08 (0.26), residues: 463 sheet: 0.37 (0.37), residues: 222 loop : -1.79 (0.25), residues: 528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.059 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 227 average time/residue: 1.0462 time to fit residues: 258.1545 Evaluate side-chains 230 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 14 residues processed: 9 average time/residue: 0.3556 time to fit residues: 5.5208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 84 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 GLN A 356 ASN A 380 ASN B 52 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9913 Z= 0.205 Angle : 0.521 6.442 13467 Z= 0.254 Chirality : 0.043 0.174 1480 Planarity : 0.004 0.037 1740 Dihedral : 8.753 161.579 1359 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 3.25 % 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: -0.78 (0.25), residues: 1213 helix: 0.33 (0.26), residues: 449 sheet: 0.57 (0.38), residues: 211 loop : -1.68 (0.25), residues: 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 226 average time/residue: 1.0394 time to fit residues: 256.4562 Evaluate side-chains 226 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 15 residues processed: 9 average time/residue: 0.4733 time to fit residues: 6.7011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 356 ASN B 100 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 9913 Z= 0.422 Angle : 0.603 6.898 13467 Z= 0.296 Chirality : 0.047 0.193 1480 Planarity : 0.004 0.040 1740 Dihedral : 9.172 166.525 1359 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 3.16 % 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: -0.88 (0.24), residues: 1213 helix: 0.15 (0.26), residues: 454 sheet: 0.53 (0.38), residues: 211 loop : -1.68 (0.25), residues: 548 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 1.184 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 22 residues processed: 221 average time/residue: 1.0126 time to fit residues: 243.9726 Evaluate side-chains 219 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 7 average time/residue: 0.1812 time to fit residues: 3.4176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 70 optimal weight: 0.3980 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 206 ASN A 356 ASN A 380 ASN B 99 ASN B 131 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9913 Z= 0.196 Angle : 0.532 7.058 13467 Z= 0.260 Chirality : 0.042 0.169 1480 Planarity : 0.004 0.039 1740 Dihedral : 8.844 161.316 1359 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 2.20 % 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: -0.68 (0.25), residues: 1213 helix: 0.36 (0.26), residues: 454 sheet: 0.62 (0.38), residues: 211 loop : -1.60 (0.25), residues: 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 1.135 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 215 average time/residue: 1.0259 time to fit residues: 239.9945 Evaluate side-chains 208 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1131 time to fit residues: 1.8625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 356 ASN B 52 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9913 Z= 0.241 Angle : 0.550 7.341 13467 Z= 0.267 Chirality : 0.043 0.166 1480 Planarity : 0.004 0.037 1740 Dihedral : 8.813 160.406 1359 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 1.72 % 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: -0.65 (0.25), residues: 1213 helix: 0.39 (0.26), residues: 454 sheet: 0.61 (0.38), residues: 215 loop : -1.58 (0.25), residues: 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.113 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 211 average time/residue: 1.0098 time to fit residues: 232.2744 Evaluate side-chains 207 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.9799 time to fit residues: 2.4503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 732 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.123094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103452 restraints weight = 21712.653| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.48 r_work: 0.3378 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work: 0.3339 rms_B_bonded: 2.27 restraints_weight: 0.1250 r_work: 0.3317 rms_B_bonded: 2.42 restraints_weight: 0.0625 r_work: 0.3293 rms_B_bonded: 2.63 restraints_weight: 0.0312 r_work: 0.3266 rms_B_bonded: 2.91 restraints_weight: 0.0156 r_work: 0.3236 rms_B_bonded: 3.26 restraints_weight: 0.0078 r_work: 0.3202 rms_B_bonded: 3.70 restraints_weight: 0.0039 r_work: 0.3163 rms_B_bonded: 4.23 restraints_weight: 0.0020 r_work: 0.3119 rms_B_bonded: 4.87 restraints_weight: 0.0010 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9913 Z= 0.291 Angle : 0.564 7.357 13467 Z= 0.275 Chirality : 0.044 0.164 1480 Planarity : 0.004 0.039 1740 Dihedral : 8.897 160.833 1359 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 1.91 % 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: -0.68 (0.25), residues: 1213 helix: 0.33 (0.26), residues: 455 sheet: 0.60 (0.38), residues: 215 loop : -1.58 (0.25), residues: 543 =============================================================================== Job complete usr+sys time: 4387.34 seconds wall clock time: 78 minutes 10.80 seconds (4690.80 seconds total)