Starting phenix.real_space_refine on Thu Sep 18 15:34:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gyp_0095/09_2025/6gyp_0095.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gyp_0095/09_2025/6gyp_0095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gyp_0095/09_2025/6gyp_0095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gyp_0095/09_2025/6gyp_0095.map" model { file = "/net/cci-nas-00/data/ceres_data/6gyp_0095/09_2025/6gyp_0095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gyp_0095/09_2025/6gyp_0095.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 11539 2.51 5 N 2932 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17811 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4374 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 509} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3526 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4362 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 510} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4265 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 476} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 4.42, per 1000 atoms: 0.25 Number of scatterers: 17811 At special positions: 0 Unit cell: (170.66, 143.1, 97.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 3272 8.00 N 2932 7.00 C 11539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 712.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 10 sheets defined 60.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.887A pdb=" N PHE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.921A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 4.154A pdb=" N MET B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.421A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.515A pdb=" N GLU B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 153 through 173 removed outlier: 4.132A pdb=" N TRP B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 removed outlier: 3.725A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 204 through 222 Processing helix chain 'B' and resid 230 through 241 removed outlier: 4.021A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.567A pdb=" N SER B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 4.124A pdb=" N ILE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.830A pdb=" N ILE B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 385 Processing helix chain 'B' and resid 394 through 422 removed outlier: 3.712A pdb=" N PHE B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 444 removed outlier: 3.571A pdb=" N ASN B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.535A pdb=" N PHE B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.949A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 494 removed outlier: 3.741A pdb=" N GLN B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 496 No H-bonds generated for 'chain 'B' and resid 495 through 496' Processing helix chain 'B' and resid 497 through 500 removed outlier: 3.681A pdb=" N PHE B 500 " --> pdb=" O PRO B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 501 through 524 removed outlier: 3.740A pdb=" N ASP B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 523 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.910A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 560 Processing helix chain 'B' and resid 589 through 601 removed outlier: 4.110A pdb=" N ILE B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.886A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.923A pdb=" N LEU A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.752A pdb=" N LYS A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.627A pdb=" N GLU A 78 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 5.232A pdb=" N GLU A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.738A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.584A pdb=" N VAL A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.635A pdb=" N MET A 270 " --> pdb=" O MET A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.905A pdb=" N GLU A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.098A pdb=" N ILE A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.932A pdb=" N ASN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.857A pdb=" N VAL A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'C' and resid 56 through 74 removed outlier: 4.010A pdb=" N ASP C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 removed outlier: 4.452A pdb=" N GLU C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU C 106 " --> pdb=" O TRP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.762A pdb=" N SER C 111 " --> pdb=" O GLN C 107 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 4.065A pdb=" N SER C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.973A pdb=" N ALA C 148 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 173 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 185 through 193 removed outlier: 3.542A pdb=" N HIS C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 223 removed outlier: 3.616A pdb=" N CYS C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 241 removed outlier: 4.149A pdb=" N VAL C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.570A pdb=" N ASP C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 266 Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.690A pdb=" N ILE C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 341 through 357 removed outlier: 3.534A pdb=" N TYR C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 385 Processing helix chain 'C' and resid 393 through 422 removed outlier: 3.573A pdb=" N ARG C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.969A pdb=" N ALA C 448 " --> pdb=" O ASN C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.732A pdb=" N HIS C 456 " --> pdb=" O PHE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 477 removed outlier: 3.779A pdb=" N ILE C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 494 Processing helix chain 'C' and resid 495 through 496 No H-bonds generated for 'chain 'C' and resid 495 through 496' Processing helix chain 'C' and resid 497 through 500 removed outlier: 3.535A pdb=" N PHE C 500 " --> pdb=" O PRO C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 497 through 500' Processing helix chain 'C' and resid 501 through 524 removed outlier: 3.583A pdb=" N ASP C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 552 removed outlier: 3.677A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 562 Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.652A pdb=" N ASP C 605 " --> pdb=" O ASN C 602 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 606 " --> pdb=" O ILE C 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 606' Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.811A pdb=" N LYS D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 127 through 141 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 38 through 59 Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 107 through 139 removed outlier: 3.969A pdb=" N VAL E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 170 removed outlier: 4.293A pdb=" N LEU E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 207 through 222 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.690A pdb=" N THR E 285 " --> pdb=" O CYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 349 removed outlier: 3.669A pdb=" N PHE E 338 " --> pdb=" O ARG E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 377 removed outlier: 3.641A pdb=" N PHE E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 384 removed outlier: 3.524A pdb=" N ASN E 382 " --> pdb=" O ASN E 379 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY E 384 " --> pdb=" O GLU E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 408 Processing helix chain 'E' and resid 429 through 435 removed outlier: 3.996A pdb=" N VAL E 433 " --> pdb=" O LYS E 429 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN E 434 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 435' Processing helix chain 'E' and resid 436 through 444 removed outlier: 4.156A pdb=" N ASP E 440 " --> pdb=" O PHE E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 479 Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 482 through 486 removed outlier: 3.508A pdb=" N PHE E 485 " --> pdb=" O HIS E 482 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN E 486 " --> pdb=" O ASP E 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 482 through 486' Processing helix chain 'E' and resid 487 through 491 removed outlier: 3.831A pdb=" N GLY E 491 " --> pdb=" O PRO E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 503 removed outlier: 3.638A pdb=" N GLN E 496 " --> pdb=" O ASN E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 506 No H-bonds generated for 'chain 'E' and resid 504 through 506' Processing helix chain 'E' and resid 526 through 532 removed outlier: 3.572A pdb=" N PHE E 530 " --> pdb=" O ASN E 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 89 through 90 removed outlier: 4.493A pdb=" N HIS C 152 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.968A pdb=" N VAL A 140 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 169 removed outlier: 6.434A pdb=" N ILE A 168 " --> pdb=" O GLY A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.736A pdb=" N ILE A 276 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 337 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.785A pdb=" N LYS A 411 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 452 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 478 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 454 " --> pdb=" O ILE A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.097A pdb=" N THR C 50 " --> pdb=" O ASP C 528 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.502A pdb=" N PHE D 16 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE D 75 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 239 through 240 removed outlier: 3.742A pdb=" N GLN E 268 " --> pdb=" O LYS E 253 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2367 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: 2.37 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5520 1.34 - 1.46: 3975 1.46 - 1.58: 8647 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 18247 Sorted by residual: bond pdb=" CB ASP A 173 " pdb=" CG ASP A 173 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.47e+00 bond pdb=" CA GLU B 389 " pdb=" CB GLU B 389 " ideal model delta sigma weight residual 1.524 1.551 -0.028 1.31e-02 5.83e+03 4.46e+00 bond pdb=" N ASN A 371 " pdb=" CA ASN A 371 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.12e+00 bond pdb=" CB VAL A 151 " pdb=" CG1 VAL A 151 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.32e+00 bond pdb=" CB CYS D 151 " pdb=" SG CYS D 151 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.52e+00 ... (remaining 18242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 24013 2.47 - 4.94: 603 4.94 - 7.40: 73 7.40 - 9.87: 22 9.87 - 12.34: 4 Bond angle restraints: 24715 Sorted by residual: angle pdb=" C LYS A 368 " pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta sigma weight residual 121.54 132.94 -11.40 1.91e+00 2.74e-01 3.56e+01 angle pdb=" C ILE A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta sigma weight residual 126.45 135.59 -9.14 1.77e+00 3.19e-01 2.67e+01 angle pdb=" C TYR B 57 " pdb=" N LEU B 58 " pdb=" CA LEU B 58 " ideal model delta sigma weight residual 120.09 126.34 -6.25 1.25e+00 6.40e-01 2.50e+01 angle pdb=" N LYS E 260 " pdb=" CA LYS E 260 " pdb=" C LYS E 260 " ideal model delta sigma weight residual 114.75 108.84 5.91 1.26e+00 6.30e-01 2.20e+01 angle pdb=" C TYR B 335 " pdb=" N ARG B 336 " pdb=" CA ARG B 336 " ideal model delta sigma weight residual 123.47 130.47 -7.00 1.53e+00 4.27e-01 2.10e+01 ... (remaining 24710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 10252 15.32 - 30.64: 535 30.64 - 45.96: 136 45.96 - 61.28: 16 61.28 - 76.60: 15 Dihedral angle restraints: 10954 sinusoidal: 4535 harmonic: 6419 Sorted by residual: dihedral pdb=" CA ILE A 421 " pdb=" C ILE A 421 " pdb=" N THR A 422 " pdb=" CA THR A 422 " ideal model delta harmonic sigma weight residual -180.00 -142.18 -37.82 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CB CYS B 99 " pdb=" SG CYS B 99 " pdb=" SG CYS B 215 " pdb=" CB CYS B 215 " ideal model delta sinusoidal sigma weight residual 93.00 157.53 -64.53 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CA LYS A 368 " pdb=" C LYS A 368 " pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta harmonic sigma weight residual 180.00 146.38 33.62 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 10951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2386 0.080 - 0.159: 309 0.159 - 0.239: 22 0.239 - 0.318: 2 0.318 - 0.398: 1 Chirality restraints: 2720 Sorted by residual: chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CG LEU A 359 " pdb=" CB LEU A 359 " pdb=" CD1 LEU A 359 " pdb=" CD2 LEU A 359 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE A 421 " pdb=" CA ILE A 421 " pdb=" CG1 ILE A 421 " pdb=" CG2 ILE A 421 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2717 not shown) Planarity restraints: 3128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 150 " -0.026 2.00e-02 2.50e+03 1.91e-02 9.08e+00 pdb=" CG TRP A 150 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 150 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 150 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 150 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 150 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 150 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 150 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 150 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 150 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 443 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C GLN A 443 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN A 443 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 444 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 90 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C LEU E 90 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU E 90 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 91 " 0.016 2.00e-02 2.50e+03 ... (remaining 3125 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4367 2.79 - 3.32: 16220 3.32 - 3.84: 29461 3.84 - 4.37: 34632 4.37 - 4.90: 58967 Nonbonded interactions: 143647 Sorted by model distance: nonbonded pdb=" OG SER E 227 " pdb=" OE1 GLU E 230 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 78 " pdb=" OG1 THR B 464 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASP E 370 " pdb=" OG1 THR E 373 " model vdw 2.281 3.040 nonbonded pdb=" OD2 ASP B 60 " pdb=" OG1 THR B 705 " model vdw 2.301 3.040 nonbonded pdb=" O ASN E 308 " pdb=" OH TYR E 442 " model vdw 2.304 3.040 ... (remaining 143642 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 'B' and (resid 53 through 319 or resid 339 through 608)) selection = (chain 'C' and (resid 53 through 319 or resid 339 through 608)) } 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=0.00 max=1.00 mean=0.99 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: 6.170 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.850 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 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 : 0.006 0.068 18248 Z= 0.258 Angle : 0.947 12.340 24717 Z= 0.524 Chirality : 0.054 0.398 2720 Planarity : 0.007 0.065 3128 Dihedral : 10.749 76.602 6771 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.08 % Favored : 92.83 % Rotamer: Outliers : 0.50 % Allowed : 3.76 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.51 (0.13), residues: 2119 helix: -2.59 (0.11), residues: 1258 sheet: -4.60 (0.56), residues: 50 loop : -3.37 (0.17), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 95 TYR 0.035 0.002 TYR D 132 PHE 0.043 0.003 PHE A 434 TRP 0.051 0.003 TRP A 150 HIS 0.013 0.002 HIS E 43 Details of bonding type rmsd covalent geometry : bond 0.00596 (18247) covalent geometry : angle 0.94641 (24715) SS BOND : bond 0.00107 ( 1) SS BOND : angle 2.22018 ( 2) hydrogen bonds : bond 0.15413 ( 807) hydrogen bonds : angle 6.34395 ( 2367) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 530 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7784 (mtt90) cc_final: 0.6871 (tmt170) REVERT: B 97 GLU cc_start: 0.8177 (pt0) cc_final: 0.7932 (tm-30) REVERT: B 134 SER cc_start: 0.9211 (m) cc_final: 0.8915 (p) REVERT: B 291 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6504 (mtm110) REVERT: B 364 LYS cc_start: 0.8377 (mttp) cc_final: 0.8171 (mttt) REVERT: B 399 GLN cc_start: 0.7685 (tt0) cc_final: 0.6797 (tp40) REVERT: B 407 ILE cc_start: 0.7965 (tp) cc_final: 0.7642 (tp) REVERT: B 423 ASP cc_start: 0.8182 (t0) cc_final: 0.7327 (m-30) REVERT: B 444 ASN cc_start: 0.8435 (t0) cc_final: 0.8177 (t0) REVERT: B 450 SER cc_start: 0.8532 (p) cc_final: 0.8071 (p) REVERT: B 451 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7567 (mp0) REVERT: A 25 ASP cc_start: 0.8065 (t0) cc_final: 0.7742 (t0) REVERT: A 36 ILE cc_start: 0.8530 (mp) cc_final: 0.8223 (mm) REVERT: A 111 ASP cc_start: 0.8457 (m-30) cc_final: 0.8256 (m-30) REVERT: A 119 GLU cc_start: 0.7612 (tt0) cc_final: 0.7401 (tt0) REVERT: A 146 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8576 (mt-10) REVERT: A 164 ASN cc_start: 0.7831 (m110) cc_final: 0.7261 (p0) REVERT: A 282 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7300 (tmtt) REVERT: A 307 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7420 (mmm-85) REVERT: A 319 GLN cc_start: 0.7854 (mt0) cc_final: 0.7594 (mt0) REVERT: A 332 ASP cc_start: 0.8799 (p0) cc_final: 0.8548 (p0) REVERT: A 367 ILE cc_start: 0.8104 (mt) cc_final: 0.7823 (mm) REVERT: A 373 GLU cc_start: 0.7917 (tp30) cc_final: 0.7667 (tp30) REVERT: A 381 LYS cc_start: 0.8345 (tppt) cc_final: 0.7969 (mtmt) REVERT: A 384 LYS cc_start: 0.7918 (tttt) cc_final: 0.7565 (ttmm) REVERT: A 388 LYS cc_start: 0.8655 (tttt) cc_final: 0.8416 (mtpp) REVERT: A 405 LEU cc_start: 0.7371 (mt) cc_final: 0.7169 (mt) REVERT: A 409 ARG cc_start: 0.7640 (ttm170) cc_final: 0.7201 (mtp85) REVERT: A 420 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 465 GLU cc_start: 0.8362 (pt0) cc_final: 0.7767 (pt0) REVERT: A 474 GLN cc_start: 0.8391 (tm130) cc_final: 0.7861 (tm-30) REVERT: C 87 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.6808 (ptt90) REVERT: C 120 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7830 (mm-30) REVERT: C 141 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6959 (mt-10) REVERT: C 173 TYR cc_start: 0.8194 (m-80) cc_final: 0.7940 (m-80) REVERT: C 187 PRO cc_start: 0.6555 (Cg_exo) cc_final: 0.6301 (Cg_endo) REVERT: C 204 MET cc_start: 0.8825 (tpt) cc_final: 0.8602 (tpp) REVERT: C 230 ASP cc_start: 0.8738 (t0) cc_final: 0.8290 (t0) REVERT: C 280 PRO cc_start: 0.7342 (Cg_exo) cc_final: 0.7138 (Cg_endo) REVERT: C 347 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7666 (mttt) REVERT: C 367 LEU cc_start: 0.7919 (mt) cc_final: 0.7664 (tt) REVERT: C 371 ASP cc_start: 0.8574 (m-30) cc_final: 0.8203 (m-30) REVERT: C 382 TYR cc_start: 0.8594 (t80) cc_final: 0.8315 (t80) REVERT: C 411 SER cc_start: 0.8684 (m) cc_final: 0.8245 (p) REVERT: C 423 ASP cc_start: 0.8556 (t70) cc_final: 0.8137 (t0) REVERT: C 440 SER cc_start: 0.9221 (t) cc_final: 0.8973 (p) REVERT: C 451 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8094 (pt0) REVERT: C 460 MET cc_start: 0.8469 (tpt) cc_final: 0.7498 (tpp) REVERT: C 477 VAL cc_start: 0.7493 (t) cc_final: 0.7266 (m) REVERT: C 540 ILE cc_start: 0.6884 (mt) cc_final: 0.6642 (mt) REVERT: C 544 ASP cc_start: 0.8071 (m-30) cc_final: 0.7806 (m-30) REVERT: C 550 LEU cc_start: 0.7785 (tp) cc_final: 0.7544 (tp) REVERT: C 553 ASP cc_start: 0.7499 (t0) cc_final: 0.7090 (t0) REVERT: C 556 PHE cc_start: 0.7325 (m-80) cc_final: 0.6833 (m-80) REVERT: C 593 ILE cc_start: 0.8684 (mt) cc_final: 0.8189 (tp) REVERT: C 600 GLU cc_start: 0.8412 (tt0) cc_final: 0.8175 (tp30) REVERT: D 12 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 15 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8102 (mtp85) REVERT: D 17 THR cc_start: 0.9278 (m) cc_final: 0.9012 (p) REVERT: D 18 VAL cc_start: 0.8504 (t) cc_final: 0.8111 (m) REVERT: D 21 LYS cc_start: 0.8766 (tttt) cc_final: 0.8546 (ttpp) REVERT: D 98 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.7994 (ptm-80) REVERT: D 104 ASP cc_start: 0.7948 (t0) cc_final: 0.7391 (t0) REVERT: D 117 ASP cc_start: 0.7074 (t0) cc_final: 0.6873 (m-30) REVERT: D 118 SER cc_start: 0.8647 (m) cc_final: 0.8219 (p) REVERT: D 127 ASP cc_start: 0.6983 (t0) cc_final: 0.6670 (t0) REVERT: D 165 GLU cc_start: 0.7543 (pp20) cc_final: 0.7015 (pp20) REVERT: D 180 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7232 (mt-10) REVERT: D 189 GLU cc_start: 0.8173 (tp30) cc_final: 0.7933 (tp30) REVERT: E 60 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6691 (tp-100) REVERT: E 78 LEU cc_start: 0.9073 (tp) cc_final: 0.8859 (mt) REVERT: E 146 ILE cc_start: 0.8340 (tt) cc_final: 0.8044 (tp) REVERT: E 152 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7416 (tp30) REVERT: E 160 HIS cc_start: 0.6825 (t70) cc_final: 0.6605 (t70) REVERT: E 161 TRP cc_start: 0.7456 (t-100) cc_final: 0.7205 (t-100) REVERT: E 244 ARG cc_start: 0.6047 (tpp-160) cc_final: 0.5826 (tpp80) REVERT: E 251 TYR cc_start: 0.6014 (t80) cc_final: 0.3751 (t80) REVERT: E 371 GLU cc_start: 0.5961 (tp30) cc_final: 0.4732 (pt0) REVERT: E 401 PHE cc_start: 0.6309 (t80) cc_final: 0.6013 (t80) REVERT: E 409 PHE cc_start: 0.5956 (m-10) cc_final: 0.5466 (t80) outliers start: 10 outliers final: 2 residues processed: 536 average time/residue: 0.1497 time to fit residues: 117.1145 Evaluate side-chains 319 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 338 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 235 GLN B 406 GLN B 543 ASN A 23 HIS A 108 HIS A 310 ASN A 333 ASN A 335 GLN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 189 HIS C 199 ASN C 394 ASN C 399 GLN D 34 ASN D 101 ASN D 188 ASN E 143 ASN E 177 ASN E 266 HIS E 379 ASN E 383 HIS E 505 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.179504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130229 restraints weight = 24593.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127379 restraints weight = 19751.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129480 restraints weight = 19587.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129416 restraints weight = 13531.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132294 restraints weight = 11499.467| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18248 Z= 0.149 Angle : 0.623 10.222 24717 Z= 0.329 Chirality : 0.043 0.172 2720 Planarity : 0.005 0.058 3128 Dihedral : 5.743 42.331 2347 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.20 % Rotamer: Outliers : 2.26 % Allowed : 9.78 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.16), residues: 2119 helix: -1.02 (0.14), residues: 1257 sheet: -3.36 (0.85), residues: 31 loop : -2.94 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 221 TYR 0.028 0.001 TYR E 49 PHE 0.022 0.002 PHE B 476 TRP 0.026 0.002 TRP A 150 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00345 (18247) covalent geometry : angle 0.62319 (24715) SS BOND : bond 0.00147 ( 1) SS BOND : angle 1.97362 ( 2) hydrogen bonds : bond 0.04278 ( 807) hydrogen bonds : angle 4.55884 ( 2367) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 370 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7185 (tpt) REVERT: B 450 SER cc_start: 0.9044 (p) cc_final: 0.8755 (m) REVERT: B 591 ARG cc_start: 0.7662 (ttm110) cc_final: 0.7399 (mtm-85) REVERT: A 196 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8899 (pt) REVERT: A 420 GLN cc_start: 0.8751 (tm-30) cc_final: 0.7827 (tm-30) REVERT: C 357 GLN cc_start: 0.8218 (pt0) cc_final: 0.7928 (tm-30) REVERT: C 367 LEU cc_start: 0.7601 (mt) cc_final: 0.7373 (mt) REVERT: C 423 ASP cc_start: 0.8497 (t70) cc_final: 0.7998 (t0) REVERT: C 460 MET cc_start: 0.8788 (tpt) cc_final: 0.8203 (tpp) REVERT: C 477 VAL cc_start: 0.8259 (t) cc_final: 0.7848 (m) REVERT: C 517 LEU cc_start: 0.9289 (tp) cc_final: 0.9066 (mp) REVERT: C 520 LEU cc_start: 0.9100 (tp) cc_final: 0.8887 (tt) REVERT: C 540 ILE cc_start: 0.8270 (mt) cc_final: 0.8032 (mt) REVERT: C 553 ASP cc_start: 0.7965 (t0) cc_final: 0.7665 (t0) REVERT: C 554 GLU cc_start: 0.7253 (mm-30) cc_final: 0.7042 (mm-30) REVERT: D 17 THR cc_start: 0.8476 (m) cc_final: 0.8216 (p) REVERT: D 34 ASN cc_start: 0.7797 (m-40) cc_final: 0.7585 (m-40) REVERT: D 104 ASP cc_start: 0.8163 (t0) cc_final: 0.7826 (t0) REVERT: E 35 ASP cc_start: 0.7167 (m-30) cc_final: 0.6781 (t0) REVERT: E 60 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7125 (tp-100) REVERT: E 152 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7575 (tp30) REVERT: E 156 LYS cc_start: 0.8437 (mttt) cc_final: 0.7512 (tptm) REVERT: E 161 TRP cc_start: 0.8047 (t-100) cc_final: 0.7771 (t-100) REVERT: E 243 LYS cc_start: 0.8489 (mptt) cc_final: 0.8194 (mtmm) REVERT: E 249 ILE cc_start: 0.7038 (mt) cc_final: 0.6800 (mm) REVERT: E 251 TYR cc_start: 0.5107 (t80) cc_final: 0.3547 (t80) outliers start: 45 outliers final: 25 residues processed: 402 average time/residue: 0.1395 time to fit residues: 84.5678 Evaluate side-chains 310 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 193 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 154 optimal weight: 0.0970 chunk 109 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 399 GLN C 406 GLN C 543 ASN E 86 HIS E 252 HIS E 266 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.177610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127993 restraints weight = 24949.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123435 restraints weight = 17177.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125005 restraints weight = 20320.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125362 restraints weight = 13944.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129481 restraints weight = 12014.089| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18248 Z= 0.168 Angle : 0.621 11.827 24717 Z= 0.324 Chirality : 0.043 0.181 2720 Planarity : 0.004 0.049 3128 Dihedral : 5.466 53.071 2347 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.87 % Rotamer: Outliers : 3.01 % Allowed : 10.94 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.17), residues: 2119 helix: -0.43 (0.14), residues: 1258 sheet: -3.04 (0.91), residues: 31 loop : -2.69 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 221 TYR 0.020 0.001 TYR E 49 PHE 0.021 0.002 PHE B 597 TRP 0.020 0.002 TRP A 150 HIS 0.011 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00399 (18247) covalent geometry : angle 0.62099 (24715) SS BOND : bond 0.00106 ( 1) SS BOND : angle 1.28542 ( 2) hydrogen bonds : bond 0.04038 ( 807) hydrogen bonds : angle 4.28840 ( 2367) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8323 (t0) cc_final: 0.7918 (t0) REVERT: B 595 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8398 (mm-30) REVERT: A 162 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7387 (tt) REVERT: C 367 LEU cc_start: 0.7673 (mt) cc_final: 0.7370 (mt) REVERT: C 423 ASP cc_start: 0.8484 (t70) cc_final: 0.8009 (t0) REVERT: C 460 MET cc_start: 0.8815 (tpt) cc_final: 0.8241 (tpp) REVERT: D 17 THR cc_start: 0.8504 (m) cc_final: 0.8251 (p) REVERT: D 104 ASP cc_start: 0.8228 (t0) cc_final: 0.7947 (t0) REVERT: D 148 ASP cc_start: 0.7043 (t0) cc_final: 0.6830 (t0) REVERT: E 35 ASP cc_start: 0.7190 (m-30) cc_final: 0.6861 (t0) REVERT: E 60 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6902 (tp-100) REVERT: E 152 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7655 (tp30) REVERT: E 156 LYS cc_start: 0.8528 (mttt) cc_final: 0.7621 (tptp) REVERT: E 252 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.5448 (t-90) REVERT: E 376 THR cc_start: 0.8512 (p) cc_final: 0.8299 (t) REVERT: E 409 PHE cc_start: 0.7184 (t80) cc_final: 0.6664 (t80) outliers start: 60 outliers final: 39 residues processed: 353 average time/residue: 0.1369 time to fit residues: 74.4325 Evaluate side-chains 311 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 95 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 117 optimal weight: 0.0670 chunk 131 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN D 34 ASN E 86 HIS E 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118591 restraints weight = 24828.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119222 restraints weight = 21202.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120582 restraints weight = 13533.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121630 restraints weight = 11157.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121984 restraints weight = 10539.031| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18248 Z= 0.168 Angle : 0.621 12.342 24717 Z= 0.318 Chirality : 0.043 0.172 2720 Planarity : 0.004 0.044 3128 Dihedral : 5.308 58.473 2347 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.82 % Rotamer: Outliers : 3.16 % Allowed : 12.54 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.18), residues: 2119 helix: -0.08 (0.15), residues: 1265 sheet: -2.42 (0.83), residues: 43 loop : -2.53 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 221 TYR 0.020 0.001 TYR C 509 PHE 0.018 0.002 PHE C 597 TRP 0.017 0.002 TRP A 150 HIS 0.016 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00403 (18247) covalent geometry : angle 0.62082 (24715) SS BOND : bond 0.00190 ( 1) SS BOND : angle 1.55543 ( 2) hydrogen bonds : bond 0.03889 ( 807) hydrogen bonds : angle 4.12319 ( 2367) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8083 (mtt) cc_final: 0.7832 (mtt) REVERT: B 202 ASP cc_start: 0.8286 (t0) cc_final: 0.7892 (t0) REVERT: B 382 TYR cc_start: 0.7779 (m-80) cc_final: 0.7489 (m-80) REVERT: B 595 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8292 (mm-30) REVERT: A 37 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7479 (t70) REVERT: A 109 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 162 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7462 (tt) REVERT: A 373 GLU cc_start: 0.7433 (tp30) cc_final: 0.7198 (tp30) REVERT: A 378 LYS cc_start: 0.8461 (mttt) cc_final: 0.8163 (ttmm) REVERT: C 115 MET cc_start: 0.8390 (tpp) cc_final: 0.8031 (tpp) REVERT: C 367 LEU cc_start: 0.7639 (mt) cc_final: 0.7345 (mt) REVERT: C 417 MET cc_start: 0.8599 (mmm) cc_final: 0.8234 (mmt) REVERT: C 423 ASP cc_start: 0.8540 (t70) cc_final: 0.8032 (t0) REVERT: C 460 MET cc_start: 0.8859 (tpt) cc_final: 0.8626 (tpt) REVERT: D 17 THR cc_start: 0.8560 (m) cc_final: 0.8287 (p) REVERT: D 104 ASP cc_start: 0.8324 (t0) cc_final: 0.8021 (t0) REVERT: E 35 ASP cc_start: 0.7281 (m-30) cc_final: 0.6928 (t0) REVERT: E 60 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7071 (tp-100) REVERT: E 152 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7414 (tp30) REVERT: E 156 LYS cc_start: 0.8535 (mttt) cc_final: 0.7768 (ptpt) REVERT: E 230 GLU cc_start: 0.5449 (mp0) cc_final: 0.5134 (mp0) REVERT: E 409 PHE cc_start: 0.7343 (t80) cc_final: 0.6917 (t80) outliers start: 63 outliers final: 37 residues processed: 334 average time/residue: 0.1363 time to fit residues: 69.0397 Evaluate side-chains 305 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 121 optimal weight: 0.0040 chunk 131 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 170 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 201 optimal weight: 0.0060 overall best weight: 0.2408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN E 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.177906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124364 restraints weight = 24806.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121977 restraints weight = 15887.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123056 restraints weight = 12362.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123612 restraints weight = 11228.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123568 restraints weight = 10021.240| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18248 Z= 0.115 Angle : 0.581 11.551 24717 Z= 0.299 Chirality : 0.041 0.179 2720 Planarity : 0.004 0.045 3128 Dihedral : 5.046 54.655 2347 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 2.61 % Allowed : 14.05 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 2119 helix: 0.27 (0.15), residues: 1259 sheet: -2.50 (0.83), residues: 41 loop : -2.38 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 221 TYR 0.021 0.001 TYR C 509 PHE 0.014 0.001 PHE C 476 TRP 0.027 0.001 TRP E 161 HIS 0.008 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00261 (18247) covalent geometry : angle 0.58146 (24715) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.91414 ( 2) hydrogen bonds : bond 0.03567 ( 807) hydrogen bonds : angle 3.99078 ( 2367) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 0.627 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: B 119 MET cc_start: 0.7525 (ttp) cc_final: 0.7303 (mtp) REVERT: B 214 ARG cc_start: 0.8465 (ttm110) cc_final: 0.7983 (mtp85) REVERT: B 382 TYR cc_start: 0.7735 (m-80) cc_final: 0.7534 (m-80) REVERT: A 25 ASP cc_start: 0.7883 (t70) cc_final: 0.7158 (t70) REVERT: A 37 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7338 (t70) REVERT: A 134 LYS cc_start: 0.8755 (mmtm) cc_final: 0.8294 (mptt) REVERT: A 162 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7475 (tt) REVERT: A 373 GLU cc_start: 0.7406 (tp30) cc_final: 0.7177 (tp30) REVERT: A 378 LYS cc_start: 0.8333 (mttt) cc_final: 0.8115 (ttmm) REVERT: C 357 GLN cc_start: 0.8161 (pt0) cc_final: 0.7913 (tm-30) REVERT: C 367 LEU cc_start: 0.7657 (mt) cc_final: 0.7365 (mt) REVERT: C 417 MET cc_start: 0.8484 (mmm) cc_final: 0.8191 (mmt) REVERT: C 423 ASP cc_start: 0.8531 (t70) cc_final: 0.7977 (t0) REVERT: C 460 MET cc_start: 0.8776 (tpt) cc_final: 0.8570 (tpt) REVERT: C 555 MET cc_start: 0.8293 (tpp) cc_final: 0.8091 (mmm) REVERT: D 17 THR cc_start: 0.8514 (m) cc_final: 0.8206 (p) REVERT: D 21 LYS cc_start: 0.8810 (tptt) cc_final: 0.8597 (tttm) REVERT: D 104 ASP cc_start: 0.8201 (t0) cc_final: 0.7903 (t0) REVERT: E 35 ASP cc_start: 0.7272 (m-30) cc_final: 0.6854 (t0) REVERT: E 60 GLN cc_start: 0.7449 (mm-40) cc_final: 0.6964 (tp-100) REVERT: E 129 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8332 (mm) REVERT: E 152 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7406 (tp30) REVERT: E 156 LYS cc_start: 0.8497 (mttt) cc_final: 0.7638 (ptpt) REVERT: E 330 THR cc_start: 0.5723 (OUTLIER) cc_final: 0.5431 (p) outliers start: 52 outliers final: 34 residues processed: 344 average time/residue: 0.1340 time to fit residues: 70.5777 Evaluate side-chains 312 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 207 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 201 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 439 HIS C 399 GLN D 34 ASN E 86 HIS E 252 HIS E 266 HIS ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118913 restraints weight = 24748.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118983 restraints weight = 17849.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119140 restraints weight = 12524.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119550 restraints weight = 12013.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119915 restraints weight = 11310.767| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18248 Z= 0.192 Angle : 0.635 12.716 24717 Z= 0.324 Chirality : 0.043 0.173 2720 Planarity : 0.004 0.046 3128 Dihedral : 5.024 46.235 2347 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.20 % Rotamer: Outliers : 2.91 % Allowed : 14.65 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.18), residues: 2119 helix: 0.33 (0.15), residues: 1260 sheet: -2.49 (0.78), residues: 43 loop : -2.39 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 307 TYR 0.021 0.001 TYR C 509 PHE 0.020 0.002 PHE B 476 TRP 0.027 0.002 TRP E 161 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00467 (18247) covalent geometry : angle 0.63522 (24715) SS BOND : bond 0.00169 ( 1) SS BOND : angle 1.04468 ( 2) hydrogen bonds : bond 0.03838 ( 807) hydrogen bonds : angle 4.00953 ( 2367) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8095 (mtt) cc_final: 0.7356 (mpp) REVERT: B 202 ASP cc_start: 0.8224 (t0) cc_final: 0.7791 (t0) REVERT: B 214 ARG cc_start: 0.8483 (ttm110) cc_final: 0.7967 (mtp85) REVERT: B 382 TYR cc_start: 0.7792 (m-80) cc_final: 0.7466 (m-80) REVERT: B 404 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8739 (mt) REVERT: A 25 ASP cc_start: 0.8195 (t70) cc_final: 0.7625 (t70) REVERT: A 37 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7385 (t70) REVERT: A 66 MET cc_start: 0.8109 (ttt) cc_final: 0.7681 (ttm) REVERT: A 134 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8460 (mmtm) REVERT: A 373 GLU cc_start: 0.7503 (tp30) cc_final: 0.7230 (tp30) REVERT: A 378 LYS cc_start: 0.8382 (mttt) cc_final: 0.8178 (ttmm) REVERT: C 256 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8787 (mt) REVERT: C 367 LEU cc_start: 0.7774 (mt) cc_final: 0.7508 (mt) REVERT: C 417 MET cc_start: 0.8550 (mmm) cc_final: 0.8212 (mmt) REVERT: C 423 ASP cc_start: 0.8572 (t70) cc_final: 0.8020 (t0) REVERT: D 17 THR cc_start: 0.8635 (m) cc_final: 0.8344 (p) REVERT: D 104 ASP cc_start: 0.8320 (t0) cc_final: 0.8041 (t0) REVERT: E 35 ASP cc_start: 0.7316 (m-30) cc_final: 0.6973 (t0) REVERT: E 129 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8496 (mm) REVERT: E 152 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7569 (tp30) REVERT: E 156 LYS cc_start: 0.8455 (mttt) cc_final: 0.7776 (ptpt) REVERT: E 252 HIS cc_start: 0.6089 (t-170) cc_final: 0.5871 (t-90) REVERT: E 330 THR cc_start: 0.5346 (OUTLIER) cc_final: 0.5007 (p) REVERT: E 405 LYS cc_start: 0.7915 (mttm) cc_final: 0.7665 (tttt) outliers start: 58 outliers final: 42 residues processed: 319 average time/residue: 0.1342 time to fit residues: 65.8247 Evaluate side-chains 303 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 449 LYS Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 76 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 55 optimal weight: 0.0010 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS E 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120863 restraints weight = 24925.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120292 restraints weight = 14945.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119562 restraints weight = 13011.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120094 restraints weight = 12066.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120589 restraints weight = 11019.059| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18248 Z= 0.155 Angle : 0.615 12.755 24717 Z= 0.311 Chirality : 0.043 0.172 2720 Planarity : 0.004 0.044 3128 Dihedral : 4.943 42.709 2347 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 3.16 % Allowed : 14.80 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.18), residues: 2119 helix: 0.48 (0.15), residues: 1258 sheet: -2.44 (0.78), residues: 43 loop : -2.29 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 221 TYR 0.022 0.001 TYR C 509 PHE 0.027 0.001 PHE C 597 TRP 0.021 0.001 TRP E 55 HIS 0.005 0.001 HIS E 266 Details of bonding type rmsd covalent geometry : bond 0.00372 (18247) covalent geometry : angle 0.61452 (24715) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.96845 ( 2) hydrogen bonds : bond 0.03661 ( 807) hydrogen bonds : angle 3.92656 ( 2367) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8147 (mtt) cc_final: 0.7323 (mpp) REVERT: B 119 MET cc_start: 0.7575 (ttp) cc_final: 0.7362 (mtp) REVERT: B 214 ARG cc_start: 0.8458 (ttm110) cc_final: 0.7920 (mtp85) REVERT: B 382 TYR cc_start: 0.7769 (m-80) cc_final: 0.7435 (m-80) REVERT: A 37 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7402 (t70) REVERT: A 66 MET cc_start: 0.8080 (ttt) cc_final: 0.7647 (ttm) REVERT: A 181 ASP cc_start: 0.8322 (t0) cc_final: 0.8066 (t0) REVERT: A 373 GLU cc_start: 0.7668 (tp30) cc_final: 0.7368 (tp30) REVERT: C 367 LEU cc_start: 0.7769 (mt) cc_final: 0.7487 (mt) REVERT: C 417 MET cc_start: 0.8556 (mmm) cc_final: 0.8213 (mmt) REVERT: C 423 ASP cc_start: 0.8604 (t70) cc_final: 0.8022 (t0) REVERT: C 517 LEU cc_start: 0.9160 (tp) cc_final: 0.8947 (mp) REVERT: D 17 THR cc_start: 0.8627 (m) cc_final: 0.8317 (p) REVERT: D 104 ASP cc_start: 0.8295 (t0) cc_final: 0.8025 (t0) REVERT: E 35 ASP cc_start: 0.7371 (m-30) cc_final: 0.7149 (t0) REVERT: E 80 ILE cc_start: 0.8752 (mp) cc_final: 0.8526 (tp) REVERT: E 129 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8324 (mm) REVERT: E 152 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7552 (tp30) REVERT: E 156 LYS cc_start: 0.8472 (mttt) cc_final: 0.7759 (ptpt) REVERT: E 330 THR cc_start: 0.5790 (OUTLIER) cc_final: 0.5492 (p) REVERT: E 405 LYS cc_start: 0.7748 (mttm) cc_final: 0.7515 (tttt) outliers start: 63 outliers final: 44 residues processed: 314 average time/residue: 0.1388 time to fit residues: 67.1420 Evaluate side-chains 302 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 449 LYS Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 51 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 101 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 193 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN D 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.173610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116285 restraints weight = 24912.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115545 restraints weight = 18562.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116340 restraints weight = 13293.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117398 restraints weight = 12057.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117908 restraints weight = 10689.753| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18248 Z= 0.172 Angle : 0.632 13.552 24717 Z= 0.321 Chirality : 0.043 0.177 2720 Planarity : 0.004 0.053 3128 Dihedral : 4.928 38.816 2347 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 2.96 % Allowed : 15.05 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.18), residues: 2119 helix: 0.52 (0.15), residues: 1264 sheet: -2.44 (0.76), residues: 43 loop : -2.29 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 221 TYR 0.023 0.001 TYR C 509 PHE 0.017 0.002 PHE A 356 TRP 0.027 0.002 TRP E 55 HIS 0.006 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00415 (18247) covalent geometry : angle 0.63209 (24715) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.82616 ( 2) hydrogen bonds : bond 0.03738 ( 807) hydrogen bonds : angle 3.94815 ( 2367) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 268 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8292 (mtt) cc_final: 0.7951 (mtt) REVERT: B 202 ASP cc_start: 0.8256 (t0) cc_final: 0.7764 (t0) REVERT: B 382 TYR cc_start: 0.7727 (m-80) cc_final: 0.7398 (m-80) REVERT: A 37 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7412 (t70) REVERT: A 66 MET cc_start: 0.8063 (ttt) cc_final: 0.7671 (ttm) REVERT: A 163 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 373 GLU cc_start: 0.7686 (tp30) cc_final: 0.7380 (tp30) REVERT: C 103 MET cc_start: 0.8858 (mpp) cc_final: 0.8133 (mpp) REVERT: C 367 LEU cc_start: 0.7764 (mt) cc_final: 0.7501 (mt) REVERT: C 417 MET cc_start: 0.8513 (mmm) cc_final: 0.8174 (mmt) REVERT: C 423 ASP cc_start: 0.8582 (t70) cc_final: 0.8014 (t0) REVERT: D 17 THR cc_start: 0.8639 (m) cc_final: 0.8369 (p) REVERT: D 104 ASP cc_start: 0.8361 (t0) cc_final: 0.8093 (t0) REVERT: D 189 GLU cc_start: 0.8214 (tp30) cc_final: 0.7940 (tp30) REVERT: E 35 ASP cc_start: 0.7314 (m-30) cc_final: 0.7104 (t0) REVERT: E 129 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8347 (mm) REVERT: E 152 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7592 (tp30) REVERT: E 156 LYS cc_start: 0.8457 (mttt) cc_final: 0.7772 (ptpt) REVERT: E 330 THR cc_start: 0.5655 (OUTLIER) cc_final: 0.5307 (p) REVERT: E 467 ARG cc_start: 0.5123 (ttm-80) cc_final: 0.4884 (ttm-80) outliers start: 59 outliers final: 46 residues processed: 308 average time/residue: 0.1338 time to fit residues: 64.4100 Evaluate side-chains 307 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 116 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122224 restraints weight = 24776.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120963 restraints weight = 15651.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120778 restraints weight = 12689.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121656 restraints weight = 12290.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121775 restraints weight = 10816.519| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18248 Z= 0.147 Angle : 0.624 12.942 24717 Z= 0.316 Chirality : 0.042 0.180 2720 Planarity : 0.004 0.057 3128 Dihedral : 4.889 36.241 2347 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.85 % Favored : 94.10 % Rotamer: Outliers : 3.06 % Allowed : 15.35 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.18), residues: 2119 helix: 0.62 (0.15), residues: 1264 sheet: -2.50 (0.76), residues: 43 loop : -2.24 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 455 TYR 0.023 0.001 TYR C 509 PHE 0.015 0.001 PHE A 356 TRP 0.024 0.002 TRP E 55 HIS 0.005 0.001 HIS E 266 Details of bonding type rmsd covalent geometry : bond 0.00350 (18247) covalent geometry : angle 0.62386 (24715) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.75216 ( 2) hydrogen bonds : bond 0.03611 ( 807) hydrogen bonds : angle 3.88882 ( 2367) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 274 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8258 (mtt) cc_final: 0.7918 (mtt) REVERT: B 119 MET cc_start: 0.7529 (ttp) cc_final: 0.7304 (mtp) REVERT: B 202 ASP cc_start: 0.8278 (t0) cc_final: 0.7791 (t0) REVERT: B 382 TYR cc_start: 0.7657 (m-80) cc_final: 0.7373 (m-80) REVERT: A 37 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7402 (t70) REVERT: A 66 MET cc_start: 0.8133 (ttt) cc_final: 0.7730 (ttm) REVERT: A 163 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 174 ASN cc_start: 0.8306 (t0) cc_final: 0.8000 (t0) REVERT: A 181 ASP cc_start: 0.8308 (t0) cc_final: 0.8033 (t0) REVERT: A 373 GLU cc_start: 0.7658 (tp30) cc_final: 0.7396 (tp30) REVERT: A 458 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8457 (mp) REVERT: C 103 MET cc_start: 0.8861 (mpp) cc_final: 0.8179 (mpp) REVERT: C 367 LEU cc_start: 0.7769 (mt) cc_final: 0.7484 (mt) REVERT: C 423 ASP cc_start: 0.8576 (t70) cc_final: 0.7986 (t0) REVERT: D 17 THR cc_start: 0.8622 (m) cc_final: 0.8358 (p) REVERT: D 104 ASP cc_start: 0.8328 (t0) cc_final: 0.8053 (t0) REVERT: D 189 GLU cc_start: 0.8286 (tp30) cc_final: 0.7995 (tp30) REVERT: E 35 ASP cc_start: 0.7366 (m-30) cc_final: 0.7150 (t0) REVERT: E 129 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8359 (mm) REVERT: E 152 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7586 (tp30) REVERT: E 156 LYS cc_start: 0.8501 (mttt) cc_final: 0.7820 (ptpt) REVERT: E 330 THR cc_start: 0.5720 (OUTLIER) cc_final: 0.5380 (p) REVERT: E 409 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7213 (t80) REVERT: E 467 ARG cc_start: 0.5237 (ttm-80) cc_final: 0.4978 (ttm-80) outliers start: 61 outliers final: 47 residues processed: 318 average time/residue: 0.1362 time to fit residues: 67.6561 Evaluate side-chains 311 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 258 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 409 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 15 optimal weight: 0.5980 chunk 188 optimal weight: 10.0000 chunk 106 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 191 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN E 275 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127065 restraints weight = 24759.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122609 restraints weight = 18149.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124509 restraints weight = 21602.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124982 restraints weight = 13572.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126949 restraints weight = 11755.060| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18248 Z= 0.164 Angle : 0.645 13.094 24717 Z= 0.326 Chirality : 0.043 0.194 2720 Planarity : 0.004 0.057 3128 Dihedral : 4.876 34.015 2347 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 2.76 % Allowed : 16.06 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.18), residues: 2119 helix: 0.61 (0.15), residues: 1263 sheet: -3.14 (0.67), residues: 49 loop : -2.20 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 455 TYR 0.023 0.001 TYR C 509 PHE 0.017 0.002 PHE A 356 TRP 0.022 0.002 TRP E 55 HIS 0.005 0.001 HIS E 266 Details of bonding type rmsd covalent geometry : bond 0.00394 (18247) covalent geometry : angle 0.64514 (24715) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.80038 ( 2) hydrogen bonds : bond 0.03715 ( 807) hydrogen bonds : angle 3.92761 ( 2367) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 MET cc_start: 0.8268 (mtt) cc_final: 0.7937 (mtt) REVERT: B 119 MET cc_start: 0.7528 (ttp) cc_final: 0.7295 (mtp) REVERT: B 202 ASP cc_start: 0.8222 (t0) cc_final: 0.7752 (t0) REVERT: B 382 TYR cc_start: 0.7652 (m-80) cc_final: 0.7411 (m-80) REVERT: A 34 TYR cc_start: 0.7954 (m-80) cc_final: 0.7359 (m-80) REVERT: A 37 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7301 (t70) REVERT: A 66 MET cc_start: 0.8071 (ttt) cc_final: 0.7869 (ttt) REVERT: A 163 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 174 ASN cc_start: 0.8234 (t0) cc_final: 0.7952 (t0) REVERT: A 181 ASP cc_start: 0.8182 (t0) cc_final: 0.7963 (t0) REVERT: A 373 GLU cc_start: 0.7662 (tp30) cc_final: 0.7382 (tp30) REVERT: A 458 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8463 (mp) REVERT: C 103 MET cc_start: 0.8906 (mpp) cc_final: 0.8315 (mpp) REVERT: C 367 LEU cc_start: 0.7715 (mt) cc_final: 0.7470 (mt) REVERT: C 417 MET cc_start: 0.8409 (mmm) cc_final: 0.8192 (mmt) REVERT: C 423 ASP cc_start: 0.8483 (t70) cc_final: 0.7942 (t0) REVERT: D 17 THR cc_start: 0.8571 (m) cc_final: 0.8284 (p) REVERT: D 104 ASP cc_start: 0.8322 (t0) cc_final: 0.8079 (t0) REVERT: D 189 GLU cc_start: 0.8165 (tp30) cc_final: 0.7905 (tp30) REVERT: E 129 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8517 (mm) REVERT: E 152 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7605 (tp30) REVERT: E 156 LYS cc_start: 0.8430 (mttt) cc_final: 0.7824 (ptpt) REVERT: E 330 THR cc_start: 0.5424 (OUTLIER) cc_final: 0.5055 (p) REVERT: E 409 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7217 (t80) outliers start: 55 outliers final: 47 residues processed: 301 average time/residue: 0.1326 time to fit residues: 62.3493 Evaluate side-chains 304 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 409 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 210 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 175 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 474 GLN C 598 GLN D 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125622 restraints weight = 24926.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121058 restraints weight = 17902.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123177 restraints weight = 19491.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123129 restraints weight = 13822.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124677 restraints weight = 12296.181| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18248 Z= 0.139 Angle : 0.639 12.667 24717 Z= 0.321 Chirality : 0.043 0.223 2720 Planarity : 0.004 0.057 3128 Dihedral : 4.817 33.237 2347 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.20 % Rotamer: Outliers : 2.71 % Allowed : 16.06 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.18), residues: 2119 helix: 0.67 (0.15), residues: 1270 sheet: -2.76 (0.72), residues: 43 loop : -2.14 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 221 TYR 0.023 0.001 TYR C 509 PHE 0.027 0.001 PHE C 476 TRP 0.021 0.002 TRP E 55 HIS 0.007 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00332 (18247) covalent geometry : angle 0.63942 (24715) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.67384 ( 2) hydrogen bonds : bond 0.03567 ( 807) hydrogen bonds : angle 3.88980 ( 2367) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3134.87 seconds wall clock time: 55 minutes 12.62 seconds (3312.62 seconds total)