Starting phenix.real_space_refine on Mon Jun 16 00:36:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gyp_0095/06_2025/6gyp_0095.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gyp_0095/06_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_0095/06_2025/6gyp_0095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gyp_0095/06_2025/6gyp_0095.map" model { file = "/net/cci-nas-00/data/ceres_data/6gyp_0095/06_2025/6gyp_0095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gyp_0095/06_2025/6gyp_0095.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} 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: 10.28, per 1000 atoms: 0.58 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: 3.94 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.66 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: 4.84 Time building geometry restraints manager: 4.71 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: 4.040 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: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 37.550 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.810 ------------------------------------------------------------------------------- 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 : 4.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.051 0.003 TRP A 150 HIS 0.013 0.002 HIS E 43 PHE 0.043 0.003 PHE A 434 TYR 0.035 0.002 TYR D 132 ARG 0.014 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.15413 ( 807) hydrogen bonds : angle 6.34395 ( 2367) SS BOND : bond 0.00107 ( 1) SS BOND : angle 2.22018 ( 2) covalent geometry : bond 0.00596 (18247) covalent geometry : angle 0.94641 (24715) *********************** 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 : 1.997 Fit side-chains revert: symmetry clash 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: 0.8916 (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: 0.8172 (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: 0.7643 (tp) REVERT: B 423 ASP cc_start: 0.8182 (t0) cc_final: 0.7326 (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: 0.8072 (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: 0.7739 (t0) REVERT: A 36 ILE cc_start: 0.8530 (mp) cc_final: 0.8224 (mm) REVERT: A 111 ASP cc_start: 0.8457 (m-30) cc_final: 0.8257 (m-30) REVERT: A 119 GLU cc_start: 0.7612 (tt0) cc_final: 0.7402 (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: 0.7299 (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: 0.7596 (mt0) REVERT: A 332 ASP cc_start: 0.8799 (p0) cc_final: 0.8550 (p0) REVERT: A 373 GLU cc_start: 0.7917 (tp30) cc_final: 0.7666 (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: 0.7564 (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: 0.7200 (mtp85) REVERT: A 420 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 465 GLU cc_start: 0.8362 (pt0) cc_final: 0.7766 (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 101 PHE cc_start: 0.8365 (t80) cc_final: 0.8158 (t80) 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: 0.6304 (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: 0.8291 (t0) REVERT: C 280 PRO cc_start: 0.7342 (Cg_exo) cc_final: 0.7137 (Cg_endo) REVERT: C 347 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7665 (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: 0.8316 (t80) REVERT: C 387 LEU cc_start: 0.9049 (mt) cc_final: 0.8788 (mp) 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: 0.7265 (m) REVERT: C 540 ILE cc_start: 0.6884 (mt) cc_final: 0.6643 (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: 0.7547 (tp) REVERT: C 553 ASP cc_start: 0.7499 (t0) cc_final: 0.7022 (t0) REVERT: C 556 PHE cc_start: 0.7325 (m-80) cc_final: 0.6820 (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: 0.8083 (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: 0.7390 (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: 0.7016 (pp20) REVERT: D 180 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7231 (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: 0.7417 (tp30) REVERT: E 160 HIS cc_start: 0.6825 (t70) cc_final: 0.6623 (t70) REVERT: E 161 TRP cc_start: 0.7456 (t-100) cc_final: 0.7207 (t-100) REVERT: E 244 ARG cc_start: 0.6047 (tpp-160) cc_final: 0.5825 (tpp80) REVERT: E 251 TYR cc_start: 0.6014 (t80) cc_final: 0.3752 (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: 0.5465 (t80) REVERT: E 461 MET cc_start: 0.8437 (mmm) cc_final: 0.8179 (mmm) outliers start: 10 outliers final: 2 residues processed: 536 average time/residue: 0.3386 time to fit residues: 262.5653 Evaluate side-chains 324 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 2.132 ------------------------------------------------------------------------------- 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 179 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4020 r_free = 0.4020 target = 0.178011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117070 restraints weight = 24700.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120634 restraints weight = 14023.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122876 restraints weight = 10057.853| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18248 Z= 0.183 Angle : 0.647 10.864 24717 Z= 0.340 Chirality : 0.044 0.196 2720 Planarity : 0.005 0.059 3128 Dihedral : 5.796 43.934 2347 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 2.56 % Allowed : 9.73 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.16), residues: 2119 helix: -1.07 (0.13), residues: 1258 sheet: -3.88 (0.89), residues: 26 loop : -2.95 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 150 HIS 0.007 0.001 HIS A 291 PHE 0.021 0.002 PHE B 476 TYR 0.028 0.002 TYR E 49 ARG 0.013 0.001 ARG E 231 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 807) hydrogen bonds : angle 4.60007 ( 2367) SS BOND : bond 0.00599 ( 1) SS BOND : angle 1.81026 ( 2) covalent geometry : bond 0.00433 (18247) covalent geometry : angle 0.64654 (24715) *********************** 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 409 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 358 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7171 (tpt) REVERT: B 202 ASP cc_start: 0.8232 (t0) cc_final: 0.7894 (t0) REVERT: B 301 TYR cc_start: 0.9130 (t80) cc_final: 0.8861 (t80) REVERT: B 418 TYR cc_start: 0.9131 (m-80) cc_final: 0.8917 (m-80) REVERT: B 591 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7420 (mtm-85) REVERT: A 420 GLN cc_start: 0.8759 (tm-30) cc_final: 0.7823 (tm-30) REVERT: C 367 LEU cc_start: 0.7614 (mt) cc_final: 0.7297 (mt) REVERT: C 423 ASP cc_start: 0.8510 (t70) cc_final: 0.8016 (t0) REVERT: C 460 MET cc_start: 0.8839 (tpt) cc_final: 0.8205 (tpp) REVERT: C 517 LEU cc_start: 0.9261 (tp) cc_final: 0.9036 (mp) REVERT: C 520 LEU cc_start: 0.9110 (tp) cc_final: 0.8883 (tt) REVERT: C 540 ILE cc_start: 0.8147 (mt) cc_final: 0.7845 (mt) REVERT: C 550 LEU cc_start: 0.9036 (tp) cc_final: 0.8824 (tp) REVERT: C 553 ASP cc_start: 0.8085 (t0) cc_final: 0.7769 (t0) REVERT: C 554 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7146 (mm-30) REVERT: C 556 PHE cc_start: 0.6935 (m-80) cc_final: 0.6726 (m-80) REVERT: D 17 THR cc_start: 0.8554 (m) cc_final: 0.8277 (p) REVERT: D 34 ASN cc_start: 0.7768 (m-40) cc_final: 0.7510 (m-40) REVERT: D 104 ASP cc_start: 0.8240 (t0) cc_final: 0.7922 (t0) REVERT: E 35 ASP cc_start: 0.7226 (m-30) cc_final: 0.6812 (t0) REVERT: E 60 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7110 (tp-100) REVERT: E 76 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8157 (mmtt) REVERT: E 152 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7624 (tp30) REVERT: E 156 LYS cc_start: 0.8531 (mttt) cc_final: 0.7567 (tptm) REVERT: E 161 TRP cc_start: 0.7855 (t-100) cc_final: 0.7599 (t-100) REVERT: E 243 LYS cc_start: 0.8348 (mptt) cc_final: 0.8131 (mtmm) REVERT: E 249 ILE cc_start: 0.7342 (mt) cc_final: 0.7111 (mm) REVERT: E 251 TYR cc_start: 0.5204 (t80) cc_final: 0.3570 (t80) outliers start: 51 outliers final: 29 residues processed: 396 average time/residue: 0.2886 time to fit residues: 172.7614 Evaluate side-chains 311 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 1.999 ------------------------------------------------------------------------------- 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 304 SER 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 299 LYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 325 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 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 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 76 LYS Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 280 ILE 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 207 optimal weight: 30.0000 chunk 195 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 187 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 203 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125413 restraints weight = 24610.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121237 restraints weight = 16946.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.122073 restraints weight = 22523.709| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18248 Z= 0.197 Angle : 0.648 12.802 24717 Z= 0.335 Chirality : 0.044 0.190 2720 Planarity : 0.004 0.050 3128 Dihedral : 5.552 56.589 2347 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 3.01 % Allowed : 10.99 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.17), residues: 2119 helix: -0.43 (0.14), residues: 1263 sheet: -3.72 (0.93), residues: 26 loop : -2.67 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 150 HIS 0.011 0.001 HIS A 291 PHE 0.021 0.002 PHE B 597 TYR 0.020 0.002 TYR E 49 ARG 0.016 0.001 ARG E 221 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 807) hydrogen bonds : angle 4.30457 ( 2367) SS BOND : bond 0.00053 ( 1) SS BOND : angle 1.26857 ( 2) covalent geometry : bond 0.00468 (18247) covalent geometry : angle 0.64779 (24715) *********************** 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 368 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8418 (t0) cc_final: 0.8036 (t0) REVERT: B 301 TYR cc_start: 0.9145 (t80) cc_final: 0.8863 (t80) REVERT: B 595 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8419 (mm-30) REVERT: A 162 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7459 (tt) REVERT: A 373 GLU cc_start: 0.7155 (tp30) cc_final: 0.6953 (tp30) REVERT: C 367 LEU cc_start: 0.7674 (mt) cc_final: 0.7378 (mt) REVERT: C 423 ASP cc_start: 0.8533 (t70) cc_final: 0.8037 (t0) REVERT: C 459 VAL cc_start: 0.9526 (m) cc_final: 0.9326 (p) REVERT: C 460 MET cc_start: 0.8856 (tpt) cc_final: 0.8644 (tpt) REVERT: D 17 THR cc_start: 0.8542 (m) cc_final: 0.8280 (p) REVERT: D 104 ASP cc_start: 0.8334 (t0) cc_final: 0.8084 (t0) REVERT: E 35 ASP cc_start: 0.7324 (m-30) cc_final: 0.7004 (t0) REVERT: E 60 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7021 (tp-100) REVERT: E 76 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8163 (mmtt) REVERT: E 152 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7687 (tp30) REVERT: E 156 LYS cc_start: 0.8518 (mttt) cc_final: 0.7633 (tptp) REVERT: E 228 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: E 252 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5545 (t-90) REVERT: E 376 THR cc_start: 0.8453 (p) cc_final: 0.8248 (t) REVERT: E 409 PHE cc_start: 0.7245 (t80) cc_final: 0.6719 (t80) outliers start: 60 outliers final: 41 residues processed: 349 average time/residue: 0.2923 time to fit residues: 155.8578 Evaluate side-chains 313 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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 367 LEU 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 27 ASN 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 305 VAL Chi-restraints excluded: chain A residue 325 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 367 ILE 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 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 545 ILE 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 76 LYS Chi-restraints excluded: chain E residue 228 PHE 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 414 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 188 optimal weight: 40.0000 chunk 121 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 144 optimal weight: 0.0010 chunk 183 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS C 399 GLN D 34 ASN E 86 HIS E 266 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.126895 restraints weight = 24868.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122259 restraints weight = 18259.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124274 restraints weight = 21209.938| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18248 Z= 0.175 Angle : 0.625 12.526 24717 Z= 0.321 Chirality : 0.043 0.189 2720 Planarity : 0.004 0.048 3128 Dihedral : 5.362 55.107 2347 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 3.41 % Allowed : 12.64 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 2119 helix: -0.07 (0.15), residues: 1263 sheet: -2.95 (0.82), residues: 38 loop : -2.48 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 150 HIS 0.017 0.001 HIS A 291 PHE 0.018 0.002 PHE C 597 TYR 0.018 0.001 TYR E 49 ARG 0.006 0.000 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 807) hydrogen bonds : angle 4.15048 ( 2367) SS BOND : bond 0.00148 ( 1) SS BOND : angle 1.41196 ( 2) covalent geometry : bond 0.00420 (18247) covalent geometry : angle 0.62451 (24715) *********************** 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 351 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 283 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8429 (t0) cc_final: 0.8054 (t0) REVERT: B 301 TYR cc_start: 0.9136 (t80) cc_final: 0.8863 (t80) REVERT: B 382 TYR cc_start: 0.7781 (m-80) cc_final: 0.7428 (m-80) REVERT: B 595 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8328 (mm-30) REVERT: A 37 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7524 (t70) REVERT: A 373 GLU cc_start: 0.7412 (tp30) cc_final: 0.7167 (tp30) REVERT: C 103 MET cc_start: 0.8266 (mpp) cc_final: 0.7909 (mpp) REVERT: C 367 LEU cc_start: 0.7658 (mt) cc_final: 0.7352 (mt) REVERT: C 423 ASP cc_start: 0.8560 (t70) cc_final: 0.8041 (t0) REVERT: D 17 THR cc_start: 0.8521 (m) cc_final: 0.8248 (p) REVERT: D 21 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8688 (tttp) REVERT: D 104 ASP cc_start: 0.8340 (t0) cc_final: 0.8014 (t0) REVERT: E 35 ASP cc_start: 0.7341 (m-30) cc_final: 0.6992 (t0) REVERT: E 60 GLN cc_start: 0.7403 (mm-40) cc_final: 0.7135 (tp-100) REVERT: E 76 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8231 (mmtt) REVERT: E 152 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7733 (tp30) REVERT: E 156 LYS cc_start: 0.8460 (mttt) cc_final: 0.7612 (tptp) REVERT: E 228 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5251 (m-10) REVERT: E 230 GLU cc_start: 0.5439 (mp0) cc_final: 0.5168 (mp0) REVERT: E 409 PHE cc_start: 0.7180 (t80) cc_final: 0.6849 (t80) outliers start: 68 outliers final: 45 residues processed: 329 average time/residue: 0.2935 time to fit residues: 149.1828 Evaluate side-chains 306 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 418 TYR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU 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 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 367 ILE 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 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 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 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 166 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 228 PHE 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 159 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 116 optimal weight: 0.0980 chunk 37 optimal weight: 0.0000 chunk 129 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN B 219 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN E 86 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118176 restraints weight = 24887.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122722 restraints weight = 14956.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124218 restraints weight = 10143.963| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18248 Z= 0.120 Angle : 0.581 11.560 24717 Z= 0.298 Chirality : 0.041 0.194 2720 Planarity : 0.004 0.045 3128 Dihedral : 5.083 51.036 2347 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 2.81 % Allowed : 13.90 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2119 helix: 0.27 (0.15), residues: 1257 sheet: -2.64 (0.80), residues: 41 loop : -2.36 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 55 HIS 0.008 0.001 HIS A 291 PHE 0.019 0.001 PHE B 476 TYR 0.022 0.001 TYR C 509 ARG 0.006 0.000 ARG E 221 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 807) hydrogen bonds : angle 3.98183 ( 2367) SS BOND : bond 0.00027 ( 1) SS BOND : angle 1.09790 ( 2) covalent geometry : bond 0.00274 (18247) covalent geometry : angle 0.58140 (24715) *********************** 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 348 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 2.006 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: B 103 MET cc_start: 0.7839 (mtt) cc_final: 0.7357 (mpp) REVERT: B 202 ASP cc_start: 0.8196 (t0) cc_final: 0.7882 (t0) REVERT: B 301 TYR cc_start: 0.9157 (t80) cc_final: 0.8884 (t80) REVERT: B 382 TYR cc_start: 0.7715 (m-80) cc_final: 0.7503 (m-80) REVERT: A 25 ASP cc_start: 0.8023 (t70) cc_final: 0.7403 (t70) REVERT: A 37 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7482 (t70) REVERT: A 134 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8406 (mmtm) REVERT: A 291 HIS cc_start: 0.7001 (t-170) cc_final: 0.6797 (t70) REVERT: A 373 GLU cc_start: 0.7539 (tp30) cc_final: 0.7286 (tp30) REVERT: C 103 MET cc_start: 0.8333 (mpp) cc_final: 0.7834 (mpp) REVERT: C 367 LEU cc_start: 0.7681 (mt) cc_final: 0.7383 (mt) REVERT: C 417 MET cc_start: 0.8511 (mmm) cc_final: 0.8152 (mmt) REVERT: C 423 ASP cc_start: 0.8546 (t70) cc_final: 0.7980 (t0) REVERT: D 17 THR cc_start: 0.8595 (m) cc_final: 0.8279 (p) REVERT: D 104 ASP cc_start: 0.8313 (t0) cc_final: 0.8021 (t0) REVERT: D 148 ASP cc_start: 0.6943 (t0) cc_final: 0.6558 (t0) REVERT: E 35 ASP cc_start: 0.7250 (m-30) cc_final: 0.6888 (t0) REVERT: E 76 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8174 (mmtt) REVERT: E 152 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7659 (tp30) REVERT: E 330 THR cc_start: 0.5799 (OUTLIER) cc_final: 0.5504 (p) REVERT: E 401 PHE cc_start: 0.6198 (t80) cc_final: 0.5116 (t80) outliers start: 56 outliers final: 40 residues processed: 327 average time/residue: 0.2842 time to fit residues: 142.9919 Evaluate side-chains 306 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 2.086 ------------------------------------------------------------------------------- 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 459 VAL 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 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 196 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 334 LEU 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 367 ILE 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 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 D residue 162 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 LYS 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 414 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 33 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 160 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 0.0370 chunk 155 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 543 ASN E 86 HIS ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.177590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128292 restraints weight = 24865.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124834 restraints weight = 17860.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125919 restraints weight = 21626.405| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18248 Z= 0.147 Angle : 0.596 12.344 24717 Z= 0.304 Chirality : 0.042 0.189 2720 Planarity : 0.004 0.046 3128 Dihedral : 4.963 46.143 2347 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 3.21 % Allowed : 14.30 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2119 helix: 0.41 (0.15), residues: 1258 sheet: -2.53 (0.78), residues: 43 loop : -2.33 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 161 HIS 0.005 0.001 HIS E 266 PHE 0.015 0.001 PHE B 264 TYR 0.021 0.001 TYR C 509 ARG 0.006 0.000 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 807) hydrogen bonds : angle 3.93449 ( 2367) SS BOND : bond 0.00041 ( 1) SS BOND : angle 1.04899 ( 2) covalent geometry : bond 0.00351 (18247) covalent geometry : angle 0.59620 (24715) *********************** 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 347 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.7624 (ttp) cc_final: 0.7407 (mtp) REVERT: B 202 ASP cc_start: 0.8290 (t0) cc_final: 0.7972 (t0) REVERT: B 301 TYR cc_start: 0.9116 (t80) cc_final: 0.8835 (t80) REVERT: B 382 TYR cc_start: 0.7764 (m-80) cc_final: 0.7513 (m-80) REVERT: B 404 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8865 (mt) REVERT: A 37 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7369 (t70) REVERT: A 163 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7899 (mp) REVERT: A 373 GLU cc_start: 0.7495 (tp30) cc_final: 0.7213 (tp30) REVERT: C 367 LEU cc_start: 0.7709 (mt) cc_final: 0.7419 (mt) REVERT: C 417 MET cc_start: 0.8386 (mmm) cc_final: 0.8166 (mmt) REVERT: C 423 ASP cc_start: 0.8544 (t70) cc_final: 0.7987 (t0) REVERT: D 17 THR cc_start: 0.8597 (m) cc_final: 0.8308 (p) REVERT: D 104 ASP cc_start: 0.8298 (t0) cc_final: 0.8053 (t0) REVERT: E 35 ASP cc_start: 0.7294 (m-30) cc_final: 0.6974 (t0) REVERT: E 76 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8212 (mptt) REVERT: E 129 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8613 (mm) REVERT: E 152 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7664 (tp30) REVERT: E 330 THR cc_start: 0.5275 (OUTLIER) cc_final: 0.4943 (p) REVERT: E 405 LYS cc_start: 0.7731 (mttm) cc_final: 0.7474 (tttt) outliers start: 64 outliers final: 45 residues processed: 323 average time/residue: 0.2930 time to fit residues: 144.4249 Evaluate side-chains 313 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 343 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU 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 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 334 LEU 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 364 VAL Chi-restraints excluded: chain A residue 367 ILE 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 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 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 162 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 LYS 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 414 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 154 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 598 GLN E 86 HIS ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120121 restraints weight = 24848.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120043 restraints weight = 18392.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120345 restraints weight = 12982.271| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18248 Z= 0.167 Angle : 0.610 12.863 24717 Z= 0.310 Chirality : 0.043 0.186 2720 Planarity : 0.004 0.042 3128 Dihedral : 4.927 41.223 2347 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 3.26 % Allowed : 15.10 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2119 helix: 0.50 (0.15), residues: 1255 sheet: -2.40 (0.78), residues: 43 loop : -2.32 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 161 HIS 0.005 0.001 HIS E 266 PHE 0.028 0.001 PHE C 597 TYR 0.022 0.001 TYR C 509 ARG 0.005 0.000 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 807) hydrogen bonds : angle 3.93180 ( 2367) SS BOND : bond 0.00227 ( 1) SS BOND : angle 0.96095 ( 2) covalent geometry : bond 0.00401 (18247) covalent geometry : angle 0.61017 (24715) *********************** 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 340 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 275 time to evaluate : 2.199 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: 0.7909 (mtt) cc_final: 0.7428 (mpp) REVERT: B 202 ASP cc_start: 0.8294 (t0) cc_final: 0.7988 (t0) REVERT: B 301 TYR cc_start: 0.9156 (t80) cc_final: 0.8888 (t80) REVERT: B 382 TYR cc_start: 0.7849 (m-80) cc_final: 0.7458 (m-80) REVERT: A 37 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7375 (t70) REVERT: A 373 GLU cc_start: 0.7616 (tp30) cc_final: 0.7305 (tp30) REVERT: C 367 LEU cc_start: 0.7768 (mt) cc_final: 0.7482 (mt) REVERT: C 417 MET cc_start: 0.8507 (mmm) cc_final: 0.8249 (mmt) REVERT: C 423 ASP cc_start: 0.8588 (t70) cc_final: 0.8024 (t0) REVERT: D 17 THR cc_start: 0.8600 (m) cc_final: 0.8323 (p) REVERT: D 104 ASP cc_start: 0.8342 (t0) cc_final: 0.8103 (t0) REVERT: E 76 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8231 (mmtt) REVERT: E 129 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8475 (mm) REVERT: E 152 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7664 (tp30) REVERT: E 330 THR cc_start: 0.5521 (OUTLIER) cc_final: 0.5174 (p) outliers start: 65 outliers final: 53 residues processed: 318 average time/residue: 0.2916 time to fit residues: 141.7913 Evaluate side-chains 315 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 459 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 37 ASP 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 195 THR 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 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU 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 364 VAL Chi-restraints excluded: chain A residue 367 ILE 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 176 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 371 ASP 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 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 76 LYS 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 29 optimal weight: 0.0060 chunk 171 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 191 optimal weight: 5.9990 chunk 104 optimal weight: 0.0470 chunk 132 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.178422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117969 restraints weight = 24870.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123054 restraints weight = 14752.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123712 restraints weight = 10294.361| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18248 Z= 0.123 Angle : 0.587 12.694 24717 Z= 0.299 Chirality : 0.041 0.188 2720 Planarity : 0.004 0.053 3128 Dihedral : 4.812 37.843 2347 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 3.21 % Allowed : 15.45 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2119 helix: 0.68 (0.15), residues: 1254 sheet: -2.31 (0.78), residues: 43 loop : -2.23 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 161 HIS 0.005 0.001 HIS B 456 PHE 0.025 0.001 PHE B 476 TYR 0.022 0.001 TYR C 509 ARG 0.005 0.000 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 807) hydrogen bonds : angle 3.84770 ( 2367) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.97942 ( 2) covalent geometry : bond 0.00286 (18247) covalent geometry : angle 0.58677 (24715) *********************** 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 349 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 285 time to evaluate : 2.042 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: B 103 MET cc_start: 0.8018 (mtt) cc_final: 0.7369 (mpp) REVERT: B 301 TYR cc_start: 0.9122 (t80) cc_final: 0.8849 (t80) REVERT: B 382 TYR cc_start: 0.7805 (m-80) cc_final: 0.7436 (m-80) REVERT: B 459 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8850 (t) REVERT: A 37 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7276 (t70) REVERT: A 373 GLU cc_start: 0.7699 (tp30) cc_final: 0.7380 (tp30) REVERT: C 367 LEU cc_start: 0.7732 (mt) cc_final: 0.7464 (mt) REVERT: C 417 MET cc_start: 0.8517 (mmm) cc_final: 0.8085 (mmt) REVERT: C 423 ASP cc_start: 0.8512 (t70) cc_final: 0.7955 (t0) REVERT: D 17 THR cc_start: 0.8536 (m) cc_final: 0.8281 (p) REVERT: D 104 ASP cc_start: 0.8306 (t0) cc_final: 0.8051 (t0) REVERT: D 120 ASP cc_start: 0.9165 (m-30) cc_final: 0.8953 (m-30) REVERT: D 189 GLU cc_start: 0.8093 (tp30) cc_final: 0.7804 (tp30) REVERT: E 49 TYR cc_start: 0.8616 (p90) cc_final: 0.8187 (p90) REVERT: E 76 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8200 (mmtt) REVERT: E 152 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7652 (tp30) REVERT: E 330 THR cc_start: 0.5870 (OUTLIER) cc_final: 0.5573 (p) outliers start: 64 outliers final: 50 residues processed: 328 average time/residue: 0.3062 time to fit residues: 156.6320 Evaluate side-chains 317 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 2.214 ------------------------------------------------------------------------------- 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 459 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 37 ASP 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 196 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU 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 364 VAL Chi-restraints excluded: chain A residue 367 ILE 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 A residue 478 ILE Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 371 ASP 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 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 76 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 157 LEU 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 17 optimal weight: 0.2980 chunk 173 optimal weight: 0.0970 chunk 185 optimal weight: 8.9990 chunk 35 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 84 optimal weight: 0.0270 chunk 149 optimal weight: 0.6980 chunk 201 optimal weight: 0.0020 chunk 102 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 0.1444 ------------------------------------------------------------------------------- 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** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.180213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131163 restraints weight = 24805.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126794 restraints weight = 18494.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129187 restraints weight = 20238.423| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18248 Z= 0.106 Angle : 0.582 12.386 24717 Z= 0.294 Chirality : 0.041 0.191 2720 Planarity : 0.003 0.058 3128 Dihedral : 4.688 33.967 2347 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 2.81 % Allowed : 15.76 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2119 helix: 0.88 (0.15), residues: 1253 sheet: -2.09 (0.80), residues: 43 loop : -2.19 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 161 HIS 0.006 0.001 HIS B 456 PHE 0.022 0.001 PHE B 476 TYR 0.021 0.001 TYR C 509 ARG 0.004 0.000 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 807) hydrogen bonds : angle 3.79066 ( 2367) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.76937 ( 2) covalent geometry : bond 0.00237 (18247) covalent geometry : angle 0.58211 (24715) *********************** 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 354 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ASN cc_start: 0.8772 (t0) cc_final: 0.8399 (t0) REVERT: B 103 MET cc_start: 0.7953 (mtt) cc_final: 0.7355 (mpp) REVERT: B 214 ARG cc_start: 0.8458 (ttm110) cc_final: 0.7871 (mtp85) REVERT: B 301 TYR cc_start: 0.9055 (t80) cc_final: 0.8778 (t80) REVERT: B 382 TYR cc_start: 0.7705 (m-80) cc_final: 0.7359 (m-80) REVERT: A 34 TYR cc_start: 0.7945 (m-80) cc_final: 0.7358 (m-80) REVERT: A 37 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6917 (t70) REVERT: A 163 LEU cc_start: 0.7928 (mp) cc_final: 0.7707 (mp) REVERT: A 373 GLU cc_start: 0.7640 (tp30) cc_final: 0.7331 (tp30) REVERT: C 103 MET cc_start: 0.8434 (mpp) cc_final: 0.7864 (mpp) REVERT: C 357 GLN cc_start: 0.8242 (pt0) cc_final: 0.8040 (tm-30) REVERT: C 367 LEU cc_start: 0.7729 (mt) cc_final: 0.7393 (mt) REVERT: C 417 MET cc_start: 0.8500 (mmm) cc_final: 0.8122 (mmt) REVERT: C 423 ASP cc_start: 0.8499 (t70) cc_final: 0.7926 (t0) REVERT: C 540 ILE cc_start: 0.7487 (mt) cc_final: 0.7218 (mt) REVERT: C 555 MET cc_start: 0.8442 (mmm) cc_final: 0.8210 (tpt) REVERT: D 104 ASP cc_start: 0.8195 (t0) cc_final: 0.7980 (t0) REVERT: D 120 ASP cc_start: 0.9065 (m-30) cc_final: 0.8817 (m-30) REVERT: D 189 GLU cc_start: 0.8328 (tp30) cc_final: 0.7978 (tp30) REVERT: E 49 TYR cc_start: 0.8721 (p90) cc_final: 0.8300 (p90) REVERT: E 76 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8213 (mmtt) REVERT: E 152 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7595 (tp30) REVERT: E 161 TRP cc_start: 0.6600 (t60) cc_final: 0.6163 (t60) REVERT: E 330 THR cc_start: 0.5536 (OUTLIER) cc_final: 0.5190 (p) REVERT: E 409 PHE cc_start: 0.7086 (t80) cc_final: 0.6109 (t80) outliers start: 56 outliers final: 47 residues processed: 337 average time/residue: 0.3876 time to fit residues: 207.0003 Evaluate side-chains 325 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 2.587 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 37 ASP 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 196 ILE Chi-restraints excluded: chain A residue 303 TYR 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 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU 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 367 ILE 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 316 VAL Chi-restraints excluded: chain C residue 371 ASP 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 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 76 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 330 THR 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 135 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 203 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 146 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN E 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.175676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125510 restraints weight = 25076.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123583 restraints weight = 18309.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125394 restraints weight = 18927.295| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4140 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= 0.160 Angle : 0.632 13.451 24717 Z= 0.318 Chirality : 0.043 0.172 2720 Planarity : 0.004 0.054 3128 Dihedral : 4.750 30.531 2347 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 3.11 % Allowed : 15.81 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2119 helix: 0.78 (0.15), residues: 1264 sheet: -1.95 (0.85), residues: 37 loop : -2.14 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 161 HIS 0.005 0.001 HIS E 266 PHE 0.047 0.002 PHE E 457 TYR 0.022 0.001 TYR C 509 ARG 0.005 0.000 ARG E 455 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 807) hydrogen bonds : angle 3.85180 ( 2367) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.93041 ( 2) covalent geometry : bond 0.00388 (18247) covalent geometry : angle 0.63158 (24715) ********************** 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 329 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 267 time to evaluate : 5.510 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: 0.8108 (mtt) cc_final: 0.7414 (mpp) REVERT: B 133 ILE cc_start: 0.8640 (tt) cc_final: 0.8294 (tt) REVERT: B 202 ASP cc_start: 0.8242 (t0) cc_final: 0.7843 (t0) REVERT: B 214 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7884 (mtp85) REVERT: B 301 TYR cc_start: 0.9101 (t80) cc_final: 0.8804 (t80) REVERT: A 37 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.7006 (t70) REVERT: A 373 GLU cc_start: 0.7535 (tp30) cc_final: 0.7285 (tp30) REVERT: C 103 MET cc_start: 0.8368 (mpp) cc_final: 0.7951 (mpp) REVERT: C 367 LEU cc_start: 0.7689 (mt) cc_final: 0.7381 (mt) REVERT: C 417 MET cc_start: 0.8444 (mmm) cc_final: 0.8008 (mmt) REVERT: C 423 ASP cc_start: 0.8493 (t70) cc_final: 0.7952 (t0) REVERT: D 31 ASN cc_start: 0.8247 (m-40) cc_final: 0.7827 (m-40) REVERT: D 104 ASP cc_start: 0.8400 (t0) cc_final: 0.8187 (t0) REVERT: D 189 GLU cc_start: 0.8222 (tp30) cc_final: 0.7907 (tp30) REVERT: E 49 TYR cc_start: 0.8815 (p90) cc_final: 0.8287 (p90) REVERT: E 76 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8273 (mmtt) REVERT: E 152 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7572 (tp30) REVERT: E 330 THR cc_start: 0.5403 (OUTLIER) cc_final: 0.5042 (p) REVERT: E 409 PHE cc_start: 0.7231 (t80) cc_final: 0.6327 (t80) outliers start: 62 outliers final: 49 residues processed: 309 average time/residue: 0.4942 time to fit residues: 238.3747 Evaluate side-chains 314 residues out of total 2014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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 459 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 37 ASP 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 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 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU 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 367 ILE 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 A residue 478 ILE 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 371 ASP 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 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 62 ILE Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 157 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 7 optimal weight: 0.9990 chunk 148 optimal weight: 0.0060 chunk 152 optimal weight: 0.4980 chunk 100 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 171 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.177753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127681 restraints weight = 24949.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122712 restraints weight = 18359.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125253 restraints weight = 19749.491| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18248 Z= 0.135 Angle : 0.619 13.253 24717 Z= 0.313 Chirality : 0.042 0.180 2720 Planarity : 0.004 0.055 3128 Dihedral : 4.725 28.992 2347 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 2.71 % Allowed : 16.16 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 2119 helix: 0.86 (0.15), residues: 1258 sheet: -2.42 (0.75), residues: 43 loop : -2.10 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 161 HIS 0.006 0.001 HIS B 456 PHE 0.043 0.001 PHE E 457 TYR 0.022 0.001 TYR C 509 ARG 0.004 0.000 ARG E 455 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 807) hydrogen bonds : angle 3.82051 ( 2367) SS BOND : bond 0.00114 ( 1) SS BOND : angle 0.81119 ( 2) covalent geometry : bond 0.00323 (18247) covalent geometry : angle 0.61886 (24715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6570.59 seconds wall clock time: 118 minutes 14.22 seconds (7094.22 seconds total)