Starting phenix.real_space_refine on Tue Sep 24 23:22:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/09_2024/6r81_4749_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/09_2024/6r81_4749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/09_2024/6r81_4749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/09_2024/6r81_4749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/09_2024/6r81_4749_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/09_2024/6r81_4749_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 5668 2.51 5 N 1479 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8861 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4405 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4392 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 17, 'TRANS': 551} Chain breaks: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.61, per 1000 atoms: 0.63 Number of scatterers: 8861 At special positions: 0 Unit cell: (75.26, 90.1, 137.8, 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 35 16.00 P 6 15.00 Mg 2 11.99 O 1671 8.00 N 1479 7.00 C 5668 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 - 3.00 Amino acid : True - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 64.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.598A pdb=" N ARG A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 57 removed outlier: 4.403A pdb=" N LYS A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 3.670A pdb=" N THR A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 79 removed outlier: 4.036A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 109 removed outlier: 4.104A pdb=" N TYR A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 4.175A pdb=" N PHE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 159 removed outlier: 3.918A pdb=" N THR A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.512A pdb=" N VAL A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.746A pdb=" N ALA A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 4.187A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.503A pdb=" N GLN A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.658A pdb=" N TYR A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 269 removed outlier: 4.216A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.876A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.527A pdb=" N VAL A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 320 removed outlier: 3.856A pdb=" N GLN A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N MET A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.550A pdb=" N PHE A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 481 through 496 removed outlier: 3.519A pdb=" N ARG A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 removed outlier: 4.033A pdb=" N SER A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.720A pdb=" N ALA A 565 " --> pdb=" O HIS A 561 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.634A pdb=" N GLN A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 589 removed outlier: 4.314A pdb=" N ASN A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.600A pdb=" N ARG B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 58 removed outlier: 4.404A pdb=" N LYS B 28 " --> pdb=" O PRO B 24 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.674A pdb=" N THR B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 79 removed outlier: 4.217A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 4.101A pdb=" N TYR B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.175A pdb=" N PHE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 159 removed outlier: 3.911A pdb=" N THR B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 4.515A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.758A pdb=" N ALA B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 4.198A pdb=" N GLU B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.508A pdb=" N GLN B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 221 through 234 removed outlier: 3.658A pdb=" N TYR B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 269 removed outlier: 4.219A pdb=" N ALA B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.878A pdb=" N SER B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.535A pdb=" N LEU B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 320 removed outlier: 3.861A pdb=" N GLN B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N MET B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 removed outlier: 3.759A pdb=" N PHE B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 481 through 493 removed outlier: 3.520A pdb=" N ARG B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 removed outlier: 4.034A pdb=" N SER B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 559 through 567 removed outlier: 3.723A pdb=" N ALA B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 579 removed outlier: 3.634A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.739A pdb=" N GLU B 585 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364 removed outlier: 4.819A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 346 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA A 395 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 502 removed outlier: 6.166A pdb=" N LEU A 500 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ILE A 533 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 502 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 545 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364 removed outlier: 4.818A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 346 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA B 395 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 500 through 502 removed outlier: 6.161A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 545 " --> pdb=" O VAL B 369 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1122 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: 2.50 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1451 1.26 - 1.40: 2010 1.40 - 1.54: 5398 1.54 - 1.68: 68 1.68 - 1.82: 68 Bond restraints: 8995 Sorted by residual: bond pdb=" CA SER A 480 " pdb=" C SER A 480 " ideal model delta sigma weight residual 1.532 1.410 0.121 1.15e-02 7.56e+03 1.11e+02 bond pdb=" C THR B 381 " pdb=" O THR B 381 " ideal model delta sigma weight residual 1.237 1.125 0.111 1.19e-02 7.06e+03 8.73e+01 bond pdb=" C LYS B 380 " pdb=" O LYS B 380 " ideal model delta sigma weight residual 1.235 1.120 0.115 1.26e-02 6.30e+03 8.35e+01 bond pdb=" CA THR B 382 " pdb=" C THR B 382 " ideal model delta sigma weight residual 1.523 1.414 0.109 1.34e-02 5.57e+03 6.60e+01 bond pdb=" C ILE A 477 " pdb=" O ILE A 477 " ideal model delta sigma weight residual 1.236 1.137 0.099 1.23e-02 6.61e+03 6.45e+01 ... (remaining 8990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 12005 5.04 - 10.08: 158 10.08 - 15.12: 14 15.12 - 20.16: 5 20.16 - 25.20: 2 Bond angle restraints: 12184 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.30e+02 angle pdb=" C SER A 480 " pdb=" CA SER A 480 " pdb=" CB SER A 480 " ideal model delta sigma weight residual 114.40 89.20 25.20 1.25e+00 6.40e-01 4.06e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 117.39 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.58 17.29 1.00e+00 1.00e+00 2.99e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 121.05 15.78 1.00e+00 1.00e+00 2.49e+02 ... (remaining 12179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4731 17.89 - 35.78: 582 35.78 - 53.66: 122 53.66 - 71.55: 27 71.55 - 89.44: 16 Dihedral angle restraints: 5478 sinusoidal: 2207 harmonic: 3271 Sorted by residual: dihedral pdb=" C SER A 480 " pdb=" N SER A 480 " pdb=" CA SER A 480 " pdb=" CB SER A 480 " ideal model delta harmonic sigma weight residual -122.60 -92.81 -29.79 0 2.50e+00 1.60e-01 1.42e+02 dihedral pdb=" CA ASN A 118 " pdb=" C ASN A 118 " pdb=" N ALA A 119 " pdb=" CA ALA A 119 " ideal model delta harmonic sigma weight residual 180.00 132.04 47.96 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ASN B 118 " pdb=" C ASN B 118 " pdb=" N ALA B 119 " pdb=" CA ALA B 119 " ideal model delta harmonic sigma weight residual 180.00 132.39 47.61 0 5.00e+00 4.00e-02 9.07e+01 ... (remaining 5475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1411 0.147 - 0.294: 51 0.294 - 0.440: 6 0.440 - 0.587: 0 0.587 - 0.734: 1 Chirality restraints: 1469 Sorted by residual: chirality pdb=" CA ARG A 475 " pdb=" N ARG A 475 " pdb=" C ARG A 475 " pdb=" CB ARG A 475 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA MET B 59 " pdb=" N MET B 59 " pdb=" C MET B 59 " pdb=" CB MET B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA SER B 60 " pdb=" N SER B 60 " pdb=" C SER B 60 " pdb=" CB SER B 60 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1466 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 58 " 0.045 2.00e-02 2.50e+03 9.41e-02 8.85e+01 pdb=" C SER B 58 " -0.162 2.00e-02 2.50e+03 pdb=" O SER B 58 " 0.064 2.00e-02 2.50e+03 pdb=" N MET B 59 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 480 " -0.027 2.00e-02 2.50e+03 5.23e-02 2.73e+01 pdb=" C SER A 480 " 0.090 2.00e-02 2.50e+03 pdb=" O SER A 480 " -0.035 2.00e-02 2.50e+03 pdb=" N GLY A 481 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 474 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLU A 474 " 0.089 2.00e-02 2.50e+03 pdb=" O GLU A 474 " -0.033 2.00e-02 2.50e+03 pdb=" N ARG A 475 " -0.030 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 20 2.21 - 2.88: 3609 2.88 - 3.56: 13195 3.56 - 4.23: 19913 4.23 - 4.90: 32086 Nonbonded interactions: 68823 Sorted by model distance: nonbonded pdb=" O GLY B 374 " pdb=" NZ LYS B 380 " model vdw 1.538 3.120 nonbonded pdb=" OG SER A 480 " pdb=" N GLY A 481 " model vdw 1.887 3.120 nonbonded pdb=" O ARG B 432 " pdb=" SG CYS B 436 " model vdw 1.912 3.400 nonbonded pdb=" N GLY B 374 " pdb=" CE LYS B 380 " model vdw 1.919 3.520 nonbonded pdb=" O ARG A 432 " pdb=" SG CYS A 436 " model vdw 1.933 3.400 ... (remaining 68818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 269 or resid 282 through 586 or resid 603)) selection = (chain 'B' and (resid 9 through 269 or resid 282 through 586 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.011 0.154 8995 Z= 0.719 Angle : 1.495 25.197 12184 Z= 0.951 Chirality : 0.073 0.734 1469 Planarity : 0.009 0.094 1518 Dihedral : 16.775 89.439 3374 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.47 % Favored : 88.08 % Rotamer: Outliers : 1.25 % Allowed : 14.35 % Favored : 84.41 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.09 % 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: -5.27 (0.18), residues: 1133 helix: -3.59 (0.12), residues: 597 sheet: -2.99 (0.64), residues: 50 loop : -3.28 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 413 HIS 0.012 0.003 HIS B 141 PHE 0.027 0.004 PHE A 57 TYR 0.023 0.003 TYR B 570 ARG 0.014 0.002 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5123 (OUTLIER) cc_final: 0.4646 (t0) REVERT: A 101 GLU cc_start: 0.9225 (tp30) cc_final: 0.8826 (tp30) REVERT: A 158 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8898 (tp) REVERT: A 231 MET cc_start: 0.9205 (ttm) cc_final: 0.8862 (tpp) REVERT: A 262 LEU cc_start: 0.9228 (mm) cc_final: 0.8995 (mm) REVERT: A 295 MET cc_start: 0.9061 (tpp) cc_final: 0.8647 (tmm) REVERT: A 299 GLN cc_start: 0.9568 (mm-40) cc_final: 0.9005 (mm-40) REVERT: A 474 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 478 MET cc_start: 0.8990 (mmm) cc_final: 0.8457 (mmm) REVERT: B 145 PHE cc_start: 0.9396 (t80) cc_final: 0.8624 (t80) REVERT: B 158 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 231 MET cc_start: 0.9226 (ttm) cc_final: 0.8879 (tpp) REVERT: B 288 LEU cc_start: 0.8945 (tt) cc_final: 0.8741 (tt) REVERT: B 295 MET cc_start: 0.9109 (tpp) cc_final: 0.8486 (tmm) REVERT: B 299 GLN cc_start: 0.9470 (mm-40) cc_final: 0.8910 (mm-40) REVERT: B 413 TRP cc_start: 0.8688 (t60) cc_final: 0.7630 (t60) outliers start: 12 outliers final: 3 residues processed: 221 average time/residue: 0.1776 time to fit residues: 56.1329 Evaluate side-chains 179 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 518 GLN B 196 GLN B 518 GLN ** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8995 Z= 0.245 Angle : 0.817 9.420 12184 Z= 0.424 Chirality : 0.046 0.135 1469 Planarity : 0.005 0.057 1518 Dihedral : 9.880 79.770 1301 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.74 % Favored : 91.09 % Rotamer: Outliers : 3.85 % Allowed : 20.48 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -3.25 (0.23), residues: 1133 helix: -1.72 (0.19), residues: 616 sheet: -2.16 (0.66), residues: 50 loop : -2.65 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 413 HIS 0.010 0.002 HIS A 567 PHE 0.019 0.002 PHE A 74 TYR 0.018 0.002 TYR B 350 ARG 0.003 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9165 (t80) cc_final: 0.8638 (t80) REVERT: A 231 MET cc_start: 0.9091 (ttm) cc_final: 0.8744 (tpp) REVERT: A 258 LEU cc_start: 0.9554 (tt) cc_final: 0.9221 (tt) REVERT: A 262 LEU cc_start: 0.9242 (mm) cc_final: 0.8893 (mm) REVERT: A 299 GLN cc_start: 0.9534 (mm-40) cc_final: 0.9227 (mm110) REVERT: A 460 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7170 (t80) REVERT: A 567 HIS cc_start: 0.7532 (t70) cc_final: 0.7247 (t-90) REVERT: B 77 GLN cc_start: 0.9110 (mt0) cc_final: 0.8676 (mt0) REVERT: B 145 PHE cc_start: 0.9292 (t80) cc_final: 0.8732 (t80) REVERT: B 231 MET cc_start: 0.9163 (ttm) cc_final: 0.8905 (tpp) REVERT: B 262 LEU cc_start: 0.9196 (mm) cc_final: 0.8921 (mm) REVERT: B 295 MET cc_start: 0.9207 (tpp) cc_final: 0.8957 (tmm) REVERT: B 299 GLN cc_start: 0.9455 (mm-40) cc_final: 0.9055 (mm-40) REVERT: B 460 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7388 (t80) REVERT: B 533 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8255 (pt) REVERT: B 580 MET cc_start: 0.8252 (mtp) cc_final: 0.8000 (mtt) outliers start: 37 outliers final: 12 residues processed: 232 average time/residue: 0.1808 time to fit residues: 60.4891 Evaluate side-chains 196 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 460 PHE Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8995 Z= 0.182 Angle : 0.742 8.024 12184 Z= 0.376 Chirality : 0.043 0.171 1469 Planarity : 0.004 0.050 1518 Dihedral : 8.919 82.036 1287 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 4.68 % Allowed : 23.39 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.48 (0.24), residues: 1133 helix: -1.08 (0.20), residues: 615 sheet: -1.76 (0.64), residues: 60 loop : -2.32 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.006 0.001 HIS A 141 PHE 0.010 0.001 PHE B 348 TYR 0.012 0.001 TYR B 570 ARG 0.005 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9278 (mm-40) cc_final: 0.9031 (mm-40) REVERT: A 145 PHE cc_start: 0.9100 (t80) cc_final: 0.8681 (t80) REVERT: A 188 MET cc_start: 0.8759 (tpp) cc_final: 0.8529 (mmm) REVERT: A 191 ILE cc_start: 0.9510 (tp) cc_final: 0.8998 (tt) REVERT: A 219 SER cc_start: 0.8230 (t) cc_final: 0.7695 (p) REVERT: A 231 MET cc_start: 0.9061 (ttm) cc_final: 0.8725 (tpp) REVERT: A 256 LEU cc_start: 0.9520 (mm) cc_final: 0.9227 (mm) REVERT: A 258 LEU cc_start: 0.9488 (tt) cc_final: 0.9110 (tt) REVERT: A 262 LEU cc_start: 0.9246 (mm) cc_final: 0.8875 (mm) REVERT: A 299 GLN cc_start: 0.9518 (mm-40) cc_final: 0.9113 (mm110) REVERT: A 326 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: A 441 ARG cc_start: 0.8335 (ptp90) cc_final: 0.8103 (ptp90) REVERT: A 460 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7175 (t80) REVERT: A 567 HIS cc_start: 0.7579 (t70) cc_final: 0.7293 (t-90) REVERT: B 77 GLN cc_start: 0.9119 (mt0) cc_final: 0.8656 (mt0) REVERT: B 145 PHE cc_start: 0.9250 (t80) cc_final: 0.8655 (t80) REVERT: B 191 ILE cc_start: 0.9446 (mm) cc_final: 0.9025 (tt) REVERT: B 231 MET cc_start: 0.9146 (ttm) cc_final: 0.8822 (tpp) REVERT: B 243 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8726 (tm-30) REVERT: B 262 LEU cc_start: 0.9230 (mm) cc_final: 0.8853 (mm) REVERT: B 299 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9160 (mm110) REVERT: B 326 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8381 (tm-30) REVERT: B 433 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8778 (mt-10) REVERT: B 460 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7293 (t80) REVERT: B 580 MET cc_start: 0.8292 (mtp) cc_final: 0.8062 (mtt) outliers start: 45 outliers final: 18 residues processed: 227 average time/residue: 0.1635 time to fit residues: 54.4785 Evaluate side-chains 210 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 460 PHE Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8995 Z= 0.169 Angle : 0.719 8.965 12184 Z= 0.358 Chirality : 0.043 0.190 1469 Planarity : 0.004 0.049 1518 Dihedral : 8.587 83.440 1287 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.85 % Allowed : 25.36 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.09 (0.25), residues: 1133 helix: -0.69 (0.21), residues: 613 sheet: -1.30 (0.67), residues: 55 loop : -2.29 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.005 0.001 HIS B 141 PHE 0.008 0.001 PHE A 348 TYR 0.011 0.001 TYR B 570 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9117 (t80) cc_final: 0.8777 (t80) REVERT: A 191 ILE cc_start: 0.9528 (tp) cc_final: 0.9127 (tt) REVERT: A 196 GLN cc_start: 0.9377 (mm110) cc_final: 0.8749 (mm110) REVERT: A 219 SER cc_start: 0.8111 (t) cc_final: 0.7689 (p) REVERT: A 231 MET cc_start: 0.9061 (ttm) cc_final: 0.8718 (tpp) REVERT: A 243 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8898 (tm-30) REVERT: A 256 LEU cc_start: 0.9494 (mm) cc_final: 0.9166 (mm) REVERT: A 258 LEU cc_start: 0.9483 (tt) cc_final: 0.9064 (tt) REVERT: A 262 LEU cc_start: 0.9218 (mm) cc_final: 0.8829 (mm) REVERT: A 295 MET cc_start: 0.9154 (tmm) cc_final: 0.8797 (tmm) REVERT: A 299 GLN cc_start: 0.9528 (mm-40) cc_final: 0.9166 (mm110) REVERT: A 326 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: A 460 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7325 (t80) REVERT: A 466 ASN cc_start: 0.7982 (t0) cc_final: 0.7680 (m-40) REVERT: A 525 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8338 (mmm) REVERT: A 567 HIS cc_start: 0.7470 (t70) cc_final: 0.7186 (t-90) REVERT: B 77 GLN cc_start: 0.9103 (mt0) cc_final: 0.8605 (mt0) REVERT: B 145 PHE cc_start: 0.9238 (t80) cc_final: 0.8608 (t80) REVERT: B 191 ILE cc_start: 0.9492 (mm) cc_final: 0.9038 (tt) REVERT: B 196 GLN cc_start: 0.9424 (mm110) cc_final: 0.8981 (mm110) REVERT: B 219 SER cc_start: 0.8038 (t) cc_final: 0.7506 (p) REVERT: B 231 MET cc_start: 0.9109 (ttm) cc_final: 0.8783 (tpp) REVERT: B 243 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8720 (tm-30) REVERT: B 258 LEU cc_start: 0.9461 (tt) cc_final: 0.9008 (tt) REVERT: B 262 LEU cc_start: 0.9202 (mm) cc_final: 0.8916 (mm) REVERT: B 299 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9065 (mm110) REVERT: B 326 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8435 (tm-30) outliers start: 37 outliers final: 20 residues processed: 215 average time/residue: 0.1571 time to fit residues: 50.3484 Evaluate side-chains 212 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 0.0770 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8995 Z= 0.211 Angle : 0.737 8.726 12184 Z= 0.367 Chirality : 0.043 0.168 1469 Planarity : 0.004 0.047 1518 Dihedral : 8.303 82.158 1287 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.41 % Allowed : 25.68 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.77 (0.25), residues: 1133 helix: -0.40 (0.21), residues: 613 sheet: -1.17 (0.67), residues: 55 loop : -2.20 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 413 HIS 0.005 0.001 HIS B 141 PHE 0.009 0.001 PHE B 468 TYR 0.019 0.001 TYR A 408 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 VAL cc_start: 0.9542 (p) cc_final: 0.9288 (m) REVERT: A 77 GLN cc_start: 0.9286 (mm-40) cc_final: 0.9040 (mm-40) REVERT: A 145 PHE cc_start: 0.9068 (t80) cc_final: 0.8723 (t80) REVERT: A 191 ILE cc_start: 0.9547 (tp) cc_final: 0.9141 (tt) REVERT: A 219 SER cc_start: 0.8167 (t) cc_final: 0.7734 (p) REVERT: A 231 MET cc_start: 0.9082 (ttm) cc_final: 0.8670 (tpp) REVERT: A 243 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8921 (tm-30) REVERT: A 256 LEU cc_start: 0.9503 (mm) cc_final: 0.9222 (mm) REVERT: A 258 LEU cc_start: 0.9506 (tt) cc_final: 0.9038 (tt) REVERT: A 262 LEU cc_start: 0.9234 (mm) cc_final: 0.8855 (mm) REVERT: A 288 LEU cc_start: 0.8912 (tt) cc_final: 0.8672 (pp) REVERT: A 295 MET cc_start: 0.9188 (tmm) cc_final: 0.8842 (tmm) REVERT: A 299 GLN cc_start: 0.9565 (mm-40) cc_final: 0.9226 (mm110) REVERT: A 326 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: A 466 ASN cc_start: 0.8065 (t0) cc_final: 0.7769 (m-40) REVERT: A 567 HIS cc_start: 0.7559 (t70) cc_final: 0.7308 (t-90) REVERT: B 145 PHE cc_start: 0.9251 (t80) cc_final: 0.8653 (t80) REVERT: B 191 ILE cc_start: 0.9500 (mm) cc_final: 0.9055 (tt) REVERT: B 231 MET cc_start: 0.9131 (ttm) cc_final: 0.8734 (tpp) REVERT: B 243 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8750 (tm-30) REVERT: B 258 LEU cc_start: 0.9473 (tt) cc_final: 0.9001 (tt) REVERT: B 259 MET cc_start: 0.8543 (mmt) cc_final: 0.8322 (mmt) REVERT: B 262 LEU cc_start: 0.9251 (mm) cc_final: 0.8933 (mm) REVERT: B 295 MET cc_start: 0.9100 (tmm) cc_final: 0.8769 (tmm) REVERT: B 299 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9170 (mm110) REVERT: B 314 THR cc_start: 0.9274 (p) cc_final: 0.8942 (t) REVERT: B 326 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8369 (pp20) REVERT: B 433 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8602 (mp0) outliers start: 52 outliers final: 31 residues processed: 220 average time/residue: 0.1608 time to fit residues: 52.0401 Evaluate side-chains 216 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 105 optimal weight: 0.0980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8995 Z= 0.191 Angle : 0.748 9.809 12184 Z= 0.366 Chirality : 0.043 0.144 1469 Planarity : 0.004 0.045 1518 Dihedral : 8.245 85.453 1287 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.95 % Allowed : 29.52 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.25), residues: 1133 helix: -0.20 (0.22), residues: 607 sheet: -0.93 (0.69), residues: 55 loop : -2.08 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.005 0.001 HIS A 141 PHE 0.009 0.001 PHE A 348 TYR 0.015 0.001 TYR B 350 ARG 0.005 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9048 (t80) cc_final: 0.8718 (t80) REVERT: A 191 ILE cc_start: 0.9507 (tp) cc_final: 0.9094 (tt) REVERT: A 196 GLN cc_start: 0.9468 (mm110) cc_final: 0.8824 (mm-40) REVERT: A 219 SER cc_start: 0.8120 (t) cc_final: 0.7616 (p) REVERT: A 231 MET cc_start: 0.9096 (ttm) cc_final: 0.8622 (tpp) REVERT: A 256 LEU cc_start: 0.9498 (mm) cc_final: 0.9244 (mm) REVERT: A 290 LEU cc_start: 0.9349 (tp) cc_final: 0.8714 (pp) REVERT: A 295 MET cc_start: 0.9173 (tmm) cc_final: 0.8831 (tmm) REVERT: A 299 GLN cc_start: 0.9564 (mm-40) cc_final: 0.9233 (mm110) REVERT: A 326 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: A 466 ASN cc_start: 0.7969 (t0) cc_final: 0.7656 (t0) REVERT: A 567 HIS cc_start: 0.7542 (t70) cc_final: 0.7278 (t-90) REVERT: B 145 PHE cc_start: 0.9170 (t80) cc_final: 0.8569 (t80) REVERT: B 191 ILE cc_start: 0.9489 (mm) cc_final: 0.9045 (tt) REVERT: B 231 MET cc_start: 0.9156 (ttm) cc_final: 0.8713 (tpp) REVERT: B 243 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8723 (tm-30) REVERT: B 247 GLN cc_start: 0.9269 (tp-100) cc_final: 0.9067 (tp40) REVERT: B 258 LEU cc_start: 0.9477 (tt) cc_final: 0.8931 (tt) REVERT: B 262 LEU cc_start: 0.9252 (mm) cc_final: 0.8937 (mm) REVERT: B 295 MET cc_start: 0.9105 (tmm) cc_final: 0.8754 (tmm) REVERT: B 299 GLN cc_start: 0.9494 (mm-40) cc_final: 0.9180 (mm110) REVERT: B 314 THR cc_start: 0.9268 (p) cc_final: 0.8871 (t) REVERT: B 326 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8329 (pp20) REVERT: B 433 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8507 (mp0) outliers start: 38 outliers final: 29 residues processed: 214 average time/residue: 0.1612 time to fit residues: 50.7222 Evaluate side-chains 210 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 30.0000 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8995 Z= 0.217 Angle : 0.766 13.004 12184 Z= 0.375 Chirality : 0.044 0.217 1469 Planarity : 0.004 0.047 1518 Dihedral : 8.247 86.145 1287 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 4.89 % Allowed : 28.17 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.48 (0.25), residues: 1133 helix: -0.14 (0.22), residues: 613 sheet: -0.94 (0.70), residues: 55 loop : -2.10 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 413 HIS 0.005 0.001 HIS A 141 PHE 0.014 0.001 PHE B 57 TYR 0.017 0.001 TYR A 408 ARG 0.006 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9102 (t80) cc_final: 0.8756 (t80) REVERT: A 191 ILE cc_start: 0.9514 (tp) cc_final: 0.9086 (tt) REVERT: A 219 SER cc_start: 0.8483 (t) cc_final: 0.7957 (p) REVERT: A 256 LEU cc_start: 0.9494 (mm) cc_final: 0.9214 (mm) REVERT: A 290 LEU cc_start: 0.9369 (tp) cc_final: 0.8715 (pp) REVERT: A 295 MET cc_start: 0.9160 (tmm) cc_final: 0.8822 (tmm) REVERT: A 299 GLN cc_start: 0.9574 (mm-40) cc_final: 0.9249 (mm110) REVERT: A 326 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8317 (pp20) REVERT: A 466 ASN cc_start: 0.7929 (t0) cc_final: 0.7654 (t0) REVERT: A 567 HIS cc_start: 0.7559 (t70) cc_final: 0.7296 (t-90) REVERT: B 145 PHE cc_start: 0.9165 (t80) cc_final: 0.8635 (t80) REVERT: B 191 ILE cc_start: 0.9493 (mm) cc_final: 0.9040 (tt) REVERT: B 231 MET cc_start: 0.9161 (ttm) cc_final: 0.8654 (tpp) REVERT: B 243 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8720 (tm-30) REVERT: B 258 LEU cc_start: 0.9441 (tt) cc_final: 0.8868 (tt) REVERT: B 262 LEU cc_start: 0.9246 (mm) cc_final: 0.8881 (mm) REVERT: B 288 LEU cc_start: 0.8946 (tt) cc_final: 0.8710 (pp) REVERT: B 295 MET cc_start: 0.9108 (tmm) cc_final: 0.8770 (tmm) REVERT: B 299 GLN cc_start: 0.9536 (mm-40) cc_final: 0.9220 (mm110) REVERT: B 314 THR cc_start: 0.9276 (p) cc_final: 0.8911 (t) REVERT: B 326 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8311 (pp20) REVERT: B 355 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 433 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8469 (mp0) outliers start: 47 outliers final: 33 residues processed: 221 average time/residue: 0.1684 time to fit residues: 54.0976 Evaluate side-chains 222 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8995 Z= 0.171 Angle : 0.793 10.769 12184 Z= 0.379 Chirality : 0.043 0.231 1469 Planarity : 0.004 0.046 1518 Dihedral : 8.072 89.358 1287 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.05 % Allowed : 29.83 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.41 (0.25), residues: 1133 helix: -0.10 (0.21), residues: 619 sheet: -0.81 (0.69), residues: 55 loop : -2.08 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 413 HIS 0.003 0.001 HIS A 141 PHE 0.007 0.001 PHE B 115 TYR 0.009 0.001 TYR B 570 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8937 (mm-40) REVERT: A 145 PHE cc_start: 0.9001 (t80) cc_final: 0.8638 (t80) REVERT: A 191 ILE cc_start: 0.9495 (tp) cc_final: 0.9069 (tt) REVERT: A 196 GLN cc_start: 0.9393 (mm110) cc_final: 0.8576 (mm-40) REVERT: A 210 LEU cc_start: 0.9586 (tp) cc_final: 0.9308 (tp) REVERT: A 290 LEU cc_start: 0.9366 (tp) cc_final: 0.8678 (pp) REVERT: A 295 MET cc_start: 0.9099 (tmm) cc_final: 0.8812 (tmm) REVERT: A 299 GLN cc_start: 0.9558 (mm-40) cc_final: 0.9241 (mm110) REVERT: A 326 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8261 (pp20) REVERT: A 466 ASN cc_start: 0.7839 (t0) cc_final: 0.7568 (t0) REVERT: A 567 HIS cc_start: 0.7487 (t70) cc_final: 0.7250 (t-90) REVERT: B 145 PHE cc_start: 0.9159 (t80) cc_final: 0.8641 (t80) REVERT: B 191 ILE cc_start: 0.9479 (mm) cc_final: 0.9016 (tt) REVERT: B 196 GLN cc_start: 0.9429 (mm110) cc_final: 0.8469 (mm-40) REVERT: B 231 MET cc_start: 0.9156 (ttm) cc_final: 0.8663 (tpp) REVERT: B 243 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8838 (tm-30) REVERT: B 258 LEU cc_start: 0.9433 (tt) cc_final: 0.8841 (tt) REVERT: B 259 MET cc_start: 0.8468 (mmt) cc_final: 0.8175 (mmt) REVERT: B 262 LEU cc_start: 0.9218 (mm) cc_final: 0.8939 (mm) REVERT: B 290 LEU cc_start: 0.9341 (tp) cc_final: 0.8770 (pp) REVERT: B 295 MET cc_start: 0.9116 (tmm) cc_final: 0.8787 (tmm) REVERT: B 299 GLN cc_start: 0.9537 (mm-40) cc_final: 0.9220 (mm110) REVERT: B 326 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8228 (pp20) REVERT: B 433 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8472 (mp0) REVERT: B 485 GLN cc_start: 0.9780 (tp40) cc_final: 0.9496 (mm110) outliers start: 39 outliers final: 26 residues processed: 220 average time/residue: 0.1679 time to fit residues: 53.9013 Evaluate side-chains 218 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8995 Z= 0.228 Angle : 0.806 12.880 12184 Z= 0.389 Chirality : 0.045 0.231 1469 Planarity : 0.004 0.046 1518 Dihedral : 8.153 86.916 1287 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 3.43 % Allowed : 30.56 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.31 (0.25), residues: 1133 helix: 0.01 (0.22), residues: 619 sheet: -1.07 (0.67), residues: 60 loop : -2.06 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.004 0.001 HIS A 141 PHE 0.012 0.001 PHE B 348 TYR 0.017 0.001 TYR B 350 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9041 (t80) cc_final: 0.8671 (t80) REVERT: A 191 ILE cc_start: 0.9496 (tp) cc_final: 0.9053 (tt) REVERT: A 196 GLN cc_start: 0.9449 (mm110) cc_final: 0.8535 (mm-40) REVERT: A 290 LEU cc_start: 0.9391 (tp) cc_final: 0.8687 (pp) REVERT: A 295 MET cc_start: 0.9080 (tmm) cc_final: 0.8772 (tmm) REVERT: A 299 GLN cc_start: 0.9577 (mm-40) cc_final: 0.9272 (mm110) REVERT: A 326 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8293 (pp20) REVERT: A 567 HIS cc_start: 0.7558 (t70) cc_final: 0.7329 (t-90) REVERT: B 145 PHE cc_start: 0.9188 (t80) cc_final: 0.8698 (t80) REVERT: B 231 MET cc_start: 0.9155 (ttm) cc_final: 0.8605 (tpp) REVERT: B 243 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8845 (tm-30) REVERT: B 258 LEU cc_start: 0.9459 (tt) cc_final: 0.8859 (tt) REVERT: B 259 MET cc_start: 0.8492 (mmt) cc_final: 0.8180 (mmt) REVERT: B 262 LEU cc_start: 0.9246 (mm) cc_final: 0.8962 (mm) REVERT: B 290 LEU cc_start: 0.9318 (tp) cc_final: 0.8740 (pp) REVERT: B 295 MET cc_start: 0.9083 (tmm) cc_final: 0.8774 (tmm) REVERT: B 299 GLN cc_start: 0.9570 (mm-40) cc_final: 0.9279 (mm110) REVERT: B 314 THR cc_start: 0.9318 (p) cc_final: 0.8981 (t) REVERT: B 326 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8289 (pp20) REVERT: B 433 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8522 (mp0) REVERT: B 485 GLN cc_start: 0.9785 (tp40) cc_final: 0.9503 (mm110) outliers start: 33 outliers final: 26 residues processed: 212 average time/residue: 0.1554 time to fit residues: 48.9537 Evaluate side-chains 217 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 8.9990 chunk 74 optimal weight: 0.0980 chunk 112 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8995 Z= 0.255 Angle : 0.832 12.561 12184 Z= 0.403 Chirality : 0.045 0.223 1469 Planarity : 0.004 0.046 1518 Dihedral : 8.175 86.586 1287 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.33 % Allowed : 31.08 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.12 (0.26), residues: 1133 helix: 0.15 (0.22), residues: 606 sheet: -0.99 (0.64), residues: 65 loop : -1.89 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.004 0.001 HIS A 141 PHE 0.012 0.001 PHE B 348 TYR 0.016 0.001 TYR B 350 ARG 0.006 0.000 ARG B 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9047 (t80) cc_final: 0.8673 (t80) REVERT: A 191 ILE cc_start: 0.9528 (tp) cc_final: 0.9085 (tt) REVERT: A 290 LEU cc_start: 0.9389 (tp) cc_final: 0.8701 (pp) REVERT: A 295 MET cc_start: 0.9116 (tmm) cc_final: 0.8820 (tmm) REVERT: A 299 GLN cc_start: 0.9577 (mm-40) cc_final: 0.9295 (mm110) REVERT: A 326 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: A 355 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8738 (pp) REVERT: A 567 HIS cc_start: 0.7577 (t70) cc_final: 0.7332 (t-90) REVERT: B 145 PHE cc_start: 0.9178 (t80) cc_final: 0.8680 (t80) REVERT: B 191 ILE cc_start: 0.9458 (tp) cc_final: 0.9001 (tt) REVERT: B 231 MET cc_start: 0.9170 (ttm) cc_final: 0.8618 (tpp) REVERT: B 243 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 258 LEU cc_start: 0.9480 (tt) cc_final: 0.8870 (tt) REVERT: B 259 MET cc_start: 0.8512 (mmt) cc_final: 0.8204 (mmt) REVERT: B 262 LEU cc_start: 0.9252 (mm) cc_final: 0.8958 (mm) REVERT: B 290 LEU cc_start: 0.9354 (tp) cc_final: 0.8708 (pp) REVERT: B 295 MET cc_start: 0.9082 (tmm) cc_final: 0.8766 (tmm) REVERT: B 299 GLN cc_start: 0.9569 (mm-40) cc_final: 0.9305 (mm110) REVERT: B 314 THR cc_start: 0.9384 (p) cc_final: 0.9095 (t) REVERT: B 326 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8300 (pp20) REVERT: B 355 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8671 (pp) REVERT: B 433 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8503 (mp0) REVERT: B 528 ARG cc_start: 0.8744 (ptp90) cc_final: 0.8538 (ptp90) outliers start: 32 outliers final: 27 residues processed: 211 average time/residue: 0.1552 time to fit residues: 49.0856 Evaluate side-chains 218 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073876 restraints weight = 25752.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076891 restraints weight = 14509.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.078963 restraints weight = 9892.194| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8995 Z= 0.230 Angle : 0.832 10.758 12184 Z= 0.399 Chirality : 0.045 0.220 1469 Planarity : 0.004 0.047 1518 Dihedral : 8.158 85.781 1287 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 3.43 % Allowed : 31.08 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.04 (0.26), residues: 1133 helix: 0.22 (0.22), residues: 606 sheet: -0.66 (0.68), residues: 60 loop : -1.90 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.004 0.001 HIS A 141 PHE 0.010 0.001 PHE A 348 TYR 0.016 0.001 TYR B 408 ARG 0.003 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.76 seconds wall clock time: 34 minutes 15.74 seconds (2055.74 seconds total)