Starting phenix.real_space_refine on Tue Nov 19 02:11:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/11_2024/6gyu_0097.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/11_2024/6gyu_0097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/11_2024/6gyu_0097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/11_2024/6gyu_0097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/11_2024/6gyu_0097.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/11_2024/6gyu_0097.cif" } resolution = 3.0 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= 0.001 sd= 0.013 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 76 5.16 5 C 11745 2.51 5 N 3003 2.21 5 O 3333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18159 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4778 Classifications: {'peptide': 579} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 113 SG CYS B 14 114.872 51.167 83.797 1.00166.54 S ATOM 132 SG CYS B 17 115.332 54.747 84.272 1.00171.67 S ATOM 192 SG CYS B 24 114.285 53.545 80.324 1.00165.03 S ATOM 240 SG CYS B 30 117.693 52.033 81.734 1.00166.33 S ATOM 113 SG CYS B 14 114.872 51.167 83.797 1.00166.54 S ATOM 240 SG CYS B 30 117.693 52.033 81.734 1.00166.33 S ATOM 258 SG CYS B 33 118.325 51.880 85.570 1.00170.01 S ATOM 331 SG CYS B 42 117.527 48.058 83.334 1.00181.10 S Time building chain proxies: 9.81, per 1000 atoms: 0.54 Number of scatterers: 18159 At special positions: 0 Unit cell: (170.66, 140.98, 99.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 76 16.00 O 3333 8.00 N 3003 7.00 C 11745 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: 4.63 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 30 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 17 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 24 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 14 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 30 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 14 " Number of angles added : 12 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 11 sheets defined 60.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.244A pdb=" N LYS B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.526A pdb=" N PHE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.903A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 106 removed outlier: 4.171A pdb=" N MET B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 106 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.737A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.648A 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 154 through 174 removed outlier: 3.664A pdb=" N TRP B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.532A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 204 through 224 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.858A 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 266 Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.668A pdb=" N ILE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.537A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.986A pdb=" N LEU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 394 through 422 removed outlier: 3.527A pdb=" N PHE B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 444 through 447 removed outlier: 3.871A pdb=" N HIS B 447 " --> pdb=" O ASN B 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.744A pdb=" N ASN B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.869A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 501 through 522 Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.887A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 589 through 601 removed outlier: 3.978A pdb=" N ILE B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.621A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 606 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 607' Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.673A pdb=" N PHE A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.501A pdb=" N HIS A 23 " --> pdb=" O GLU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.543A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.509A pdb=" N GLU A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.088A 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: 3.900A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.557A 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 266 removed outlier: 3.753A pdb=" N SER A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.771A pdb=" N ILE A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.883A pdb=" N ILE A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.830A pdb=" N ASN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.797A 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 72 removed outlier: 4.022A pdb=" N ASP C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 removed outlier: 3.902A pdb=" N LEU C 106 " --> pdb=" O TRP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.540A pdb=" N PHE C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.802A pdb=" N TYR C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 153 through 173 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.998A pdb=" N GLU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 193 Processing helix chain 'C' and resid 204 through 224 Processing helix chain 'C' and resid 230 through 241 removed outlier: 4.090A pdb=" N VAL C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 249 through 266 Processing helix chain 'C' and resid 279 through 303 removed outlier: 3.792A pdb=" N ILE C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) removed outlier: 3.659A 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 356 removed outlier: 3.687A pdb=" N TYR C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 393 through 422 Processing helix chain 'C' and resid 427 through 443 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.838A pdb=" N HIS C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.601A pdb=" N HIS C 456 " --> pdb=" O PHE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 477 removed outlier: 3.566A pdb=" N GLN C 461 " --> pdb=" O PRO C 457 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 Processing helix chain 'C' and resid 501 through 524 removed outlier: 3.576A pdb=" N ASP C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 552 removed outlier: 3.693A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.587A pdb=" N GLY C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.552A pdb=" N ASP C 605 " --> pdb=" O ASN C 602 " (cutoff:3.500A) removed outlier: 3.559A 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 22 through 25 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: 3.827A pdb=" N LYS D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 127 through 141 Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 163 through 169 removed outlier: 3.672A pdb=" N THR D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) 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 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 107 through 138 removed outlier: 4.012A pdb=" N VAL E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 170 removed outlier: 4.092A 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 193 removed outlier: 3.651A pdb=" N LYS E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 223 Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.513A pdb=" N ARG E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 334 through 349 removed outlier: 3.512A pdb=" N PHE E 338 " --> pdb=" O ARG E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 377 Processing helix chain 'E' and resid 379 through 383 removed outlier: 3.658A pdb=" N HIS E 383 " --> pdb=" O GLU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 400 through 408 Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 437 through 444 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: 3.704A pdb=" N GLN E 486 " --> pdb=" O ASP E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 504 removed outlier: 3.617A pdb=" N GLN E 496 " --> pdb=" O ASN E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 507 No H-bonds generated for 'chain 'E' and resid 505 through 507' Processing helix chain 'E' and resid 526 through 533 Processing sheet with id=AA1, first strand: chain 'B' and resid 152 through 153 removed outlier: 4.216A pdb=" N HIS B 152 " --> pdb=" O ALA C 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 44 through 46 removed outlier: 3.657A pdb=" N VAL E 73 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.938A pdb=" N VAL A 140 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 168 through 169 removed outlier: 6.084A pdb=" N ILE A 168 " --> pdb=" O GLY A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.951A pdb=" N ILE A 276 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA8, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.675A pdb=" N LYS A 411 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 452 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 478 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 454 " --> pdb=" O ILE A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AB1, first strand: chain 'D' and resid 15 through 19 removed outlier: 4.111A pdb=" N ILE D 75 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 239 through 241 removed outlier: 3.735A pdb=" N GLN E 268 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 255 " --> pdb=" O HIS E 266 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2451 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: 5.76 Time building geometry restraints manager: 5.36 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: 5654 1.34 - 1.46: 4049 1.46 - 1.58: 8779 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 18597 Sorted by residual: bond pdb=" C LEU B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" CB ASP A 173 " pdb=" CG ASP A 173 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.01e+00 bond pdb=" N ASN A 371 " pdb=" CA ASN A 371 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.54e-02 4.22e+03 3.34e+00 bond pdb=" CA LYS A 299 " pdb=" C LYS A 299 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.65e+00 bond pdb=" CA LEU B 48 " pdb=" C LEU B 48 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.60e+00 ... (remaining 18592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 24772 2.96 - 5.93: 342 5.93 - 8.89: 55 8.89 - 11.85: 8 11.85 - 14.82: 3 Bond angle restraints: 25180 Sorted by residual: angle pdb=" N ASP A 37 " pdb=" CA ASP A 37 " pdb=" C ASP A 37 " ideal model delta sigma weight residual 114.62 107.54 7.08 1.14e+00 7.69e-01 3.86e+01 angle pdb=" C LYS A 368 " pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.85e+01 angle pdb=" C LEU E 93 " pdb=" N ILE E 94 " pdb=" CA ILE E 94 " ideal model delta sigma weight residual 122.72 115.30 7.42 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C ILE A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta sigma weight residual 126.45 135.88 -9.43 1.77e+00 3.19e-01 2.84e+01 angle pdb=" C ASP E 245 " pdb=" N ARG E 246 " pdb=" CA ARG E 246 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 ... (remaining 25175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 10430 15.15 - 30.30: 583 30.30 - 45.45: 142 45.45 - 60.60: 19 60.60 - 75.75: 15 Dihedral angle restraints: 11189 sinusoidal: 4638 harmonic: 6551 Sorted by residual: dihedral pdb=" CA ALA E 258 " pdb=" C ALA E 258 " pdb=" N GLU E 259 " pdb=" CA GLU E 259 " ideal model delta harmonic sigma weight residual 180.00 142.96 37.04 0 5.00e+00 4.00e-02 5.49e+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 93.00 151.56 -58.56 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CA THR E 263 " pdb=" C THR E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta harmonic sigma weight residual -180.00 -146.95 -33.05 0 5.00e+00 4.00e-02 4.37e+01 ... (remaining 11186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2134 0.060 - 0.120: 549 0.120 - 0.180: 73 0.180 - 0.240: 13 0.240 - 0.300: 3 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CA LEU B 48 " pdb=" N LEU B 48 " pdb=" C LEU B 48 " pdb=" CB LEU B 48 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CG LEU B 489 " pdb=" CB LEU B 489 " pdb=" CD1 LEU B 489 " pdb=" CD2 LEU B 489 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 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 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2769 not shown) Planarity restraints: 3187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 443 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C GLN A 443 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN A 443 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 444 " 0.018 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 2.89e-02 8.35e+00 pdb=" C LEU E 90 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU E 90 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP E 91 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 110 " 0.007 2.00e-02 2.50e+03 2.03e-02 8.21e+00 pdb=" CG TYR A 110 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 110 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 110 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 110 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 110 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 110 " -0.012 2.00e-02 2.50e+03 ... (remaining 3184 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 3418 2.77 - 3.48: 24623 3.48 - 4.19: 44184 4.19 - 4.90: 77506 Nonbonded interactions: 149733 Sorted by model distance: nonbonded pdb=" O ILE B 49 " pdb=" O THR B 50 " model vdw 1.349 3.040 nonbonded pdb=" O THR B 46 " pdb=" N LEU B 48 " model vdw 1.902 3.120 nonbonded pdb=" O MET B 43 " pdb=" CD2 LEU B 48 " model vdw 2.086 3.460 nonbonded pdb=" O ILE B 49 " pdb=" C THR B 50 " model vdw 2.168 3.270 nonbonded pdb=" O LEU B 48 " pdb=" N THR B 50 " model vdw 2.172 3.120 ... (remaining 149728 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 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 49 through 319 or resid 339 through 608)) selection = (chain 'C' and (resid 1 through 3 or resid 49 through 319 or resid 339 through 6 \ 08)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.980 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.005 0.053 18597 Z= 0.331 Angle : 0.937 14.815 25180 Z= 0.522 Chirality : 0.053 0.300 2772 Planarity : 0.007 0.059 3187 Dihedral : 10.803 75.752 6920 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.37 % Favored : 93.35 % Rotamer: Outliers : 0.74 % Allowed : 3.69 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.10 % 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: -4.30 (0.13), residues: 2166 helix: -2.48 (0.10), residues: 1276 sheet: -4.11 (0.51), residues: 56 loop : -3.17 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP E 87 HIS 0.011 0.002 HIS E 43 PHE 0.033 0.003 PHE A 434 TYR 0.042 0.002 TYR A 110 ARG 0.017 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 499 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8718 (mt) cc_final: 0.8517 (pp) REVERT: B 25 ASP cc_start: 0.7009 (t70) cc_final: 0.6644 (t0) REVERT: B 43 MET cc_start: 0.7552 (mmm) cc_final: 0.7334 (mmm) REVERT: B 97 GLU cc_start: 0.8343 (pt0) cc_final: 0.7954 (tp30) REVERT: B 103 MET cc_start: 0.8218 (mtm) cc_final: 0.7630 (mtm) REVERT: B 146 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7690 (mtp180) REVERT: B 266 ASN cc_start: 0.7630 (t0) cc_final: 0.7382 (t0) REVERT: B 291 ARG cc_start: 0.7555 (mtt180) cc_final: 0.6752 (mtm110) REVERT: B 345 TYR cc_start: 0.7960 (t80) cc_final: 0.7673 (t80) REVERT: B 354 ASP cc_start: 0.8646 (m-30) cc_final: 0.8272 (m-30) REVERT: B 423 ASP cc_start: 0.7876 (t0) cc_final: 0.7582 (t0) REVERT: B 440 SER cc_start: 0.8349 (t) cc_final: 0.7605 (p) REVERT: B 450 SER cc_start: 0.8650 (p) cc_final: 0.8255 (t) REVERT: B 461 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7616 (mm110) REVERT: B 550 LEU cc_start: 0.8566 (tp) cc_final: 0.8266 (mm) REVERT: B 560 LYS cc_start: 0.8601 (mttt) cc_final: 0.8059 (mmmm) REVERT: B 590 PHE cc_start: 0.7272 (m-10) cc_final: 0.6924 (m-10) REVERT: B 591 ARG cc_start: 0.7518 (mtt-85) cc_final: 0.7085 (ttm110) REVERT: A 36 ILE cc_start: 0.7494 (mp) cc_final: 0.6651 (mm) REVERT: A 64 ARG cc_start: 0.8634 (ttt180) cc_final: 0.8081 (ttp80) REVERT: A 78 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 82 GLN cc_start: 0.8307 (mt0) cc_final: 0.8092 (pm20) REVERT: A 203 GLN cc_start: 0.7666 (tt0) cc_final: 0.7348 (tt0) REVERT: A 265 ARG cc_start: 0.8891 (ptm-80) cc_final: 0.8405 (ptt90) REVERT: A 275 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6590 (tptm) REVERT: A 282 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7695 (tmtp) REVERT: A 310 ASN cc_start: 0.6746 (t160) cc_final: 0.6335 (m-40) REVERT: A 336 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7325 (mmtt) REVERT: A 354 LYS cc_start: 0.8774 (tppt) cc_final: 0.8521 (mptm) REVERT: A 388 LYS cc_start: 0.8644 (tttt) cc_final: 0.8301 (mtpp) REVERT: A 407 HIS cc_start: 0.9017 (m-70) cc_final: 0.8740 (m170) REVERT: A 450 ASN cc_start: 0.8108 (m-40) cc_final: 0.7879 (m-40) REVERT: A 474 GLN cc_start: 0.8421 (tm130) cc_final: 0.8212 (tp40) REVERT: C 60 ASP cc_start: 0.8195 (t70) cc_final: 0.7284 (t0) REVERT: C 119 MET cc_start: 0.8573 (ttp) cc_final: 0.8336 (ttp) REVERT: C 120 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8388 (mt-10) REVERT: C 150 LYS cc_start: 0.9055 (mttm) cc_final: 0.8710 (tptt) REVERT: C 208 MET cc_start: 0.8622 (ttp) cc_final: 0.8420 (ttp) REVERT: C 248 ASP cc_start: 0.7899 (m-30) cc_final: 0.7509 (m-30) REVERT: C 270 ASP cc_start: 0.8390 (m-30) cc_final: 0.7812 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7532 (t0) cc_final: 0.7045 (m-30) REVERT: C 280 PRO cc_start: 0.8481 (Cg_exo) cc_final: 0.8038 (Cg_endo) REVERT: C 342 GLU cc_start: 0.8402 (tp30) cc_final: 0.7579 (tm-30) REVERT: C 347 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8294 (mmtt) REVERT: C 368 LYS cc_start: 0.8749 (mttm) cc_final: 0.8474 (ptmm) REVERT: C 374 ARG cc_start: 0.8136 (ttt180) cc_final: 0.7697 (ttt180) REVERT: C 382 TYR cc_start: 0.8582 (t80) cc_final: 0.8369 (t80) REVERT: C 399 GLN cc_start: 0.7783 (tt0) cc_final: 0.7551 (tp40) REVERT: C 406 GLN cc_start: 0.8013 (mm110) cc_final: 0.7605 (mt0) REVERT: C 433 HIS cc_start: 0.8360 (t-90) cc_final: 0.8146 (t70) REVERT: C 444 ASN cc_start: 0.8237 (t0) cc_final: 0.7976 (t0) REVERT: C 550 LEU cc_start: 0.7998 (tp) cc_final: 0.7795 (tm) REVERT: D 20 LYS cc_start: 0.8201 (tttm) cc_final: 0.7807 (tppt) REVERT: D 27 LEU cc_start: 0.8138 (mt) cc_final: 0.7817 (mt) REVERT: D 29 LEU cc_start: 0.8593 (tp) cc_final: 0.8352 (tm) REVERT: D 83 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7467 (mtm110) REVERT: D 95 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7972 (mt-10) REVERT: D 98 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8580 (ttm110) REVERT: D 104 ASP cc_start: 0.8438 (t0) cc_final: 0.7631 (t0) REVERT: D 106 ASP cc_start: 0.8317 (m-30) cc_final: 0.8043 (m-30) REVERT: D 117 ASP cc_start: 0.7540 (t0) cc_final: 0.7050 (t70) REVERT: D 118 SER cc_start: 0.8635 (m) cc_final: 0.8325 (p) REVERT: D 144 LYS cc_start: 0.8146 (tppt) cc_final: 0.7453 (tptm) REVERT: D 168 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8275 (ttp-110) REVERT: E 59 ASN cc_start: 0.7940 (t0) cc_final: 0.7634 (t0) REVERT: E 83 GLU cc_start: 0.8324 (pm20) cc_final: 0.8048 (pm20) REVERT: E 93 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7425 (tt) REVERT: E 137 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7804 (mmmm) REVERT: E 163 ASP cc_start: 0.8697 (m-30) cc_final: 0.8490 (p0) REVERT: E 223 TYR cc_start: 0.7060 (m-80) cc_final: 0.6750 (m-10) REVERT: E 336 GLU cc_start: 0.8218 (pm20) cc_final: 0.7968 (tp30) REVERT: E 369 TRP cc_start: 0.7995 (m100) cc_final: 0.7753 (m100) REVERT: E 472 LEU cc_start: 0.8947 (tp) cc_final: 0.8726 (tp) REVERT: E 478 PHE cc_start: 0.8383 (m-10) cc_final: 0.8094 (m-80) REVERT: E 479 PHE cc_start: 0.8551 (m-80) cc_final: 0.8162 (m-10) REVERT: E 516 ILE cc_start: 0.8603 (mm) cc_final: 0.8369 (mm) outliers start: 15 outliers final: 5 residues processed: 509 average time/residue: 1.4379 time to fit residues: 811.7200 Evaluate side-chains 264 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 258 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.0170 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS B 235 GLN B 259 GLN B 543 ASN A 108 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN A 333 ASN A 420 GLN A 427 GLN C 82 GLN C 189 HIS C 199 ASN C 394 ASN C 543 ASN C 552 ASN D 5 ASN D 34 ASN E 54 GLN E 68 ASN E 143 ASN E 177 ASN E 191 ASN E 266 HIS E 379 ASN E 408 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18597 Z= 0.224 Angle : 0.647 10.130 25180 Z= 0.337 Chirality : 0.043 0.177 2772 Planarity : 0.005 0.050 3187 Dihedral : 5.872 74.805 2408 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.40 % Favored : 94.51 % Rotamer: Outliers : 3.00 % Allowed : 11.40 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.47 (0.16), residues: 2166 helix: -0.82 (0.13), residues: 1311 sheet: -3.67 (0.47), residues: 65 loop : -2.77 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 150 HIS 0.010 0.001 HIS A 291 PHE 0.018 0.002 PHE B 264 TYR 0.030 0.002 TYR E 49 ARG 0.006 0.001 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8869 (mt) cc_final: 0.8368 (pp) REVERT: B 97 GLU cc_start: 0.8339 (pt0) cc_final: 0.8035 (tp30) REVERT: B 146 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7703 (mtm-85) REVERT: B 291 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6811 (mtm110) REVERT: B 345 TYR cc_start: 0.8049 (t80) cc_final: 0.7703 (t80) REVERT: B 354 ASP cc_start: 0.8358 (m-30) cc_final: 0.8021 (m-30) REVERT: B 423 ASP cc_start: 0.7818 (t0) cc_final: 0.7534 (t0) REVERT: B 550 LEU cc_start: 0.8432 (tp) cc_final: 0.8179 (mm) REVERT: B 560 LYS cc_start: 0.8472 (mttt) cc_final: 0.8031 (mmmm) REVERT: A 11 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8018 (mt-10) REVERT: A 36 ILE cc_start: 0.7106 (mp) cc_final: 0.6822 (mm) REVERT: A 64 ARG cc_start: 0.8651 (ttt180) cc_final: 0.8397 (mtp85) REVERT: A 78 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 82 GLN cc_start: 0.8299 (mt0) cc_final: 0.8097 (pm20) REVERT: A 119 GLU cc_start: 0.8012 (tt0) cc_final: 0.7560 (tt0) REVERT: A 275 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6402 (tptm) REVERT: A 282 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7591 (tmtp) REVERT: A 310 ASN cc_start: 0.6767 (t0) cc_final: 0.6366 (m-40) REVERT: A 336 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7155 (mttm) REVERT: A 354 LYS cc_start: 0.8947 (tppt) cc_final: 0.8556 (tmmt) REVERT: A 388 LYS cc_start: 0.8510 (tttt) cc_final: 0.8290 (mtpp) REVERT: A 393 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7655 (ttmt) REVERT: A 394 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7788 (tm-30) REVERT: A 401 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8386 (ptpp) REVERT: A 407 HIS cc_start: 0.9064 (m-70) cc_final: 0.8806 (m-70) REVERT: C 60 ASP cc_start: 0.8242 (t70) cc_final: 0.7289 (t0) REVERT: C 120 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8381 (mt-10) REVERT: C 150 LYS cc_start: 0.9012 (mttm) cc_final: 0.8694 (tptt) REVERT: C 185 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7412 (t) REVERT: C 248 ASP cc_start: 0.7884 (m-30) cc_final: 0.7460 (m-30) REVERT: C 270 ASP cc_start: 0.8398 (m-30) cc_final: 0.7879 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7263 (t0) cc_final: 0.6802 (m-30) REVERT: C 295 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7779 (mmm160) REVERT: C 300 ASP cc_start: 0.8831 (t0) cc_final: 0.8281 (t0) REVERT: C 342 GLU cc_start: 0.8579 (tp30) cc_final: 0.7646 (tm-30) REVERT: C 368 LYS cc_start: 0.8735 (mttm) cc_final: 0.8478 (ptmm) REVERT: C 382 TYR cc_start: 0.8648 (t80) cc_final: 0.8426 (t80) REVERT: C 387 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8883 (mp) REVERT: C 433 HIS cc_start: 0.8389 (t-90) cc_final: 0.8145 (t70) REVERT: D 19 ASP cc_start: 0.8108 (t0) cc_final: 0.7904 (t0) REVERT: D 20 LYS cc_start: 0.8206 (tttm) cc_final: 0.7676 (tttt) REVERT: D 22 ILE cc_start: 0.8733 (mt) cc_final: 0.8512 (mt) REVERT: D 34 ASN cc_start: 0.7571 (m110) cc_final: 0.7368 (m-40) REVERT: D 95 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8014 (mt-10) REVERT: D 98 ARG cc_start: 0.8779 (ttp-110) cc_final: 0.8309 (ttm110) REVERT: D 104 ASP cc_start: 0.8439 (t0) cc_final: 0.7839 (t0) REVERT: D 117 ASP cc_start: 0.7783 (t0) cc_final: 0.7258 (t70) REVERT: D 165 GLU cc_start: 0.8477 (pp20) cc_final: 0.8095 (pm20) REVERT: E 31 GLN cc_start: 0.7905 (mm-40) cc_final: 0.6895 (tp40) REVERT: E 35 ASP cc_start: 0.8391 (m-30) cc_final: 0.7863 (m-30) REVERT: E 59 ASN cc_start: 0.8179 (t0) cc_final: 0.7562 (t0) REVERT: E 163 ASP cc_start: 0.8712 (m-30) cc_final: 0.8476 (p0) REVERT: E 309 LEU cc_start: 0.8925 (mp) cc_final: 0.7869 (tt) REVERT: E 329 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8417 (tm) REVERT: E 336 GLU cc_start: 0.8462 (pm20) cc_final: 0.8029 (tp30) REVERT: E 407 MET cc_start: 0.7454 (mtp) cc_final: 0.7102 (mtt) REVERT: E 434 GLN cc_start: 0.8461 (mt0) cc_final: 0.8074 (tm-30) REVERT: E 456 ASP cc_start: 0.8757 (m-30) cc_final: 0.8406 (m-30) REVERT: E 468 PHE cc_start: 0.8691 (t80) cc_final: 0.8075 (t80) REVERT: E 479 PHE cc_start: 0.8589 (m-80) cc_final: 0.8145 (m-10) outliers start: 61 outliers final: 18 residues processed: 335 average time/residue: 1.2559 time to fit residues: 476.0243 Evaluate side-chains 248 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 164 optimal weight: 0.2980 chunk 134 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN B 461 GLN B 474 GLN A 171 ASN A 348 ASN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 444 ASN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 445 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18597 Z= 0.179 Angle : 0.592 9.308 25180 Z= 0.306 Chirality : 0.042 0.168 2772 Planarity : 0.004 0.048 3187 Dihedral : 5.465 75.196 2400 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.40 % Favored : 94.51 % Rotamer: Outliers : 3.49 % Allowed : 12.63 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.45 (0.17), residues: 2166 helix: 0.03 (0.14), residues: 1301 sheet: -3.28 (0.52), residues: 65 loop : -2.41 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 150 HIS 0.019 0.001 HIS E 266 PHE 0.020 0.001 PHE E 468 TYR 0.029 0.001 TYR E 49 ARG 0.008 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8882 (mt) cc_final: 0.8309 (pp) REVERT: B 43 MET cc_start: 0.7635 (mmm) cc_final: 0.7318 (mmm) REVERT: B 97 GLU cc_start: 0.8274 (pt0) cc_final: 0.8058 (tp30) REVERT: B 135 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: B 141 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8353 (mm-30) REVERT: B 146 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7677 (mtm-85) REVERT: B 266 ASN cc_start: 0.8035 (t0) cc_final: 0.7805 (t160) REVERT: B 291 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6792 (mtm110) REVERT: B 345 TYR cc_start: 0.8054 (t80) cc_final: 0.7733 (t80) REVERT: B 354 ASP cc_start: 0.8262 (m-30) cc_final: 0.7992 (m-30) REVERT: B 423 ASP cc_start: 0.7797 (t0) cc_final: 0.7545 (t0) REVERT: B 550 LEU cc_start: 0.8515 (tp) cc_final: 0.8231 (mm) REVERT: B 560 LYS cc_start: 0.8390 (mttt) cc_final: 0.7934 (mmmm) REVERT: A 11 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8085 (mt-10) REVERT: A 46 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: A 64 ARG cc_start: 0.8620 (ttt180) cc_final: 0.8350 (mtp85) REVERT: A 66 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7835 (mtp) REVERT: A 78 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 119 GLU cc_start: 0.8032 (tt0) cc_final: 0.7573 (tt0) REVERT: A 183 CYS cc_start: 0.8232 (t) cc_final: 0.8000 (m) REVERT: A 275 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6373 (tptm) REVERT: A 282 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7587 (tttm) REVERT: A 310 ASN cc_start: 0.6709 (t0) cc_final: 0.6313 (m-40) REVERT: A 354 LYS cc_start: 0.8964 (tppt) cc_final: 0.8486 (pttt) REVERT: A 388 LYS cc_start: 0.8566 (tttt) cc_final: 0.8315 (mtpp) REVERT: A 393 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7784 (ttmt) REVERT: A 401 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8389 (ptpp) REVERT: A 407 HIS cc_start: 0.9036 (m-70) cc_final: 0.8794 (m-70) REVERT: C 60 ASP cc_start: 0.8188 (t70) cc_final: 0.7192 (t0) REVERT: C 100 MET cc_start: 0.8156 (mmm) cc_final: 0.7840 (mmp) REVERT: C 119 MET cc_start: 0.8772 (ttp) cc_final: 0.8301 (ttp) REVERT: C 120 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8406 (mt-10) REVERT: C 150 LYS cc_start: 0.8991 (mttm) cc_final: 0.8684 (tptt) REVERT: C 226 MET cc_start: 0.8617 (mtm) cc_final: 0.8192 (mtt) REVERT: C 248 ASP cc_start: 0.7881 (m-30) cc_final: 0.7446 (m-30) REVERT: C 270 ASP cc_start: 0.8400 (m-30) cc_final: 0.7884 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7176 (t0) cc_final: 0.6639 (m-30) REVERT: C 295 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7694 (mmm-85) REVERT: C 300 ASP cc_start: 0.8967 (t0) cc_final: 0.8092 (t0) REVERT: C 342 GLU cc_start: 0.8610 (tp30) cc_final: 0.7665 (tm-30) REVERT: C 368 LYS cc_start: 0.8788 (mttm) cc_final: 0.8534 (ptmm) REVERT: D 19 ASP cc_start: 0.8087 (t0) cc_final: 0.7865 (t0) REVERT: D 20 LYS cc_start: 0.8076 (tttm) cc_final: 0.7712 (tppt) REVERT: D 34 ASN cc_start: 0.7305 (m110) cc_final: 0.6870 (m-40) REVERT: D 95 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8094 (mt-10) REVERT: D 104 ASP cc_start: 0.8432 (t0) cc_final: 0.7839 (t0) REVERT: D 117 ASP cc_start: 0.7725 (t0) cc_final: 0.7272 (t70) REVERT: E 35 ASP cc_start: 0.8402 (m-30) cc_final: 0.8017 (m-30) REVERT: E 59 ASN cc_start: 0.8137 (t0) cc_final: 0.7542 (t0) REVERT: E 83 GLU cc_start: 0.8395 (pm20) cc_final: 0.7987 (pm20) REVERT: E 163 ASP cc_start: 0.8727 (m-30) cc_final: 0.8500 (p0) REVERT: E 279 PHE cc_start: 0.7961 (m-80) cc_final: 0.7682 (m-80) REVERT: E 309 LEU cc_start: 0.8853 (mp) cc_final: 0.7837 (tt) REVERT: E 425 PHE cc_start: 0.8682 (m-80) cc_final: 0.8412 (m-80) REVERT: E 434 GLN cc_start: 0.8439 (mt0) cc_final: 0.8119 (tm-30) REVERT: E 456 ASP cc_start: 0.8662 (m-30) cc_final: 0.8402 (m-30) REVERT: E 468 PHE cc_start: 0.8751 (t80) cc_final: 0.8534 (t80) REVERT: E 479 PHE cc_start: 0.8576 (m-80) cc_final: 0.8007 (m-80) REVERT: E 522 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9167 (ptmm) outliers start: 71 outliers final: 27 residues processed: 292 average time/residue: 1.2555 time to fit residues: 414.3276 Evaluate side-chains 238 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 288 ILE 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 433 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 256 HIS Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 187 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN B 542 GLN C 82 GLN C 552 ASN E 266 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18597 Z= 0.208 Angle : 0.587 9.205 25180 Z= 0.301 Chirality : 0.042 0.164 2772 Planarity : 0.004 0.046 3187 Dihedral : 5.316 74.975 2400 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 3.10 % Allowed : 14.50 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.98 (0.18), residues: 2166 helix: 0.41 (0.15), residues: 1302 sheet: -3.05 (0.52), residues: 65 loop : -2.22 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 150 HIS 0.013 0.001 HIS E 266 PHE 0.015 0.001 PHE E 520 TYR 0.027 0.001 TYR E 49 ARG 0.008 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 2.267 Fit side-chains revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8891 (mt) cc_final: 0.8307 (pp) REVERT: B 36 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7742 (mtm180) REVERT: B 43 MET cc_start: 0.7683 (mmm) cc_final: 0.7452 (mmm) REVERT: B 60 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: B 135 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: B 141 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8335 (mm-30) REVERT: B 146 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7870 (mtp180) REVERT: B 291 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6769 (mtm110) REVERT: B 345 TYR cc_start: 0.8112 (t80) cc_final: 0.7800 (t80) REVERT: B 352 ASP cc_start: 0.7994 (t0) cc_final: 0.7645 (t0) REVERT: B 354 ASP cc_start: 0.8210 (m-30) cc_final: 0.7976 (m-30) REVERT: B 423 ASP cc_start: 0.7815 (t0) cc_final: 0.7551 (t0) REVERT: B 542 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: B 550 LEU cc_start: 0.8513 (tp) cc_final: 0.8229 (mm) REVERT: B 560 LYS cc_start: 0.8330 (mttt) cc_final: 0.7891 (mmmm) REVERT: B 591 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.6941 (ttm110) REVERT: A 11 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8160 (mt-10) REVERT: A 46 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8400 (mm-30) REVERT: A 64 ARG cc_start: 0.8638 (ttt180) cc_final: 0.8367 (mtp85) REVERT: A 78 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7800 (mm-30) REVERT: A 119 GLU cc_start: 0.8012 (tt0) cc_final: 0.7556 (tt0) REVERT: A 183 CYS cc_start: 0.8209 (t) cc_final: 0.7967 (m) REVERT: A 275 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6344 (tptp) REVERT: A 282 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7641 (tttm) REVERT: A 302 SER cc_start: 0.8070 (t) cc_final: 0.7804 (t) REVERT: A 310 ASN cc_start: 0.6842 (t0) cc_final: 0.6425 (m-40) REVERT: A 354 LYS cc_start: 0.8959 (tppt) cc_final: 0.8496 (pttt) REVERT: A 388 LYS cc_start: 0.8607 (tttt) cc_final: 0.8214 (mtmt) REVERT: A 401 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8461 (ptpp) REVERT: A 407 HIS cc_start: 0.8941 (m-70) cc_final: 0.8696 (m-70) REVERT: C 60 ASP cc_start: 0.8163 (t70) cc_final: 0.7165 (t0) REVERT: C 100 MET cc_start: 0.8151 (mmm) cc_final: 0.7891 (mmp) REVERT: C 119 MET cc_start: 0.8784 (ttp) cc_final: 0.8326 (ttp) REVERT: C 120 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8329 (mt-10) REVERT: C 150 LYS cc_start: 0.9000 (mttm) cc_final: 0.8713 (tptt) REVERT: C 226 MET cc_start: 0.8652 (mtm) cc_final: 0.8252 (mtt) REVERT: C 248 ASP cc_start: 0.7899 (m-30) cc_final: 0.7463 (m-30) REVERT: C 270 ASP cc_start: 0.8408 (m-30) cc_final: 0.7892 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7324 (t0) cc_final: 0.6781 (m-30) REVERT: C 295 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7691 (mmm-85) REVERT: C 300 ASP cc_start: 0.8989 (t0) cc_final: 0.7825 (t0) REVERT: C 342 GLU cc_start: 0.8618 (tp30) cc_final: 0.7766 (tm-30) REVERT: C 368 LYS cc_start: 0.8818 (mttm) cc_final: 0.8573 (ptmm) REVERT: D 19 ASP cc_start: 0.8110 (t0) cc_final: 0.7886 (t0) REVERT: D 20 LYS cc_start: 0.8053 (tttm) cc_final: 0.7708 (tppt) REVERT: D 95 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7972 (mt-10) REVERT: D 101 ASN cc_start: 0.7980 (m-40) cc_final: 0.7733 (t0) REVERT: D 104 ASP cc_start: 0.8450 (t0) cc_final: 0.7905 (t0) REVERT: D 117 ASP cc_start: 0.7703 (t0) cc_final: 0.7257 (t70) REVERT: D 165 GLU cc_start: 0.8468 (pp20) cc_final: 0.8220 (pt0) REVERT: E 35 ASP cc_start: 0.8414 (m-30) cc_final: 0.8032 (m-30) REVERT: E 59 ASN cc_start: 0.8113 (t0) cc_final: 0.7512 (t0) REVERT: E 83 GLU cc_start: 0.8413 (pm20) cc_final: 0.7942 (pm20) REVERT: E 163 ASP cc_start: 0.8729 (m-30) cc_final: 0.8472 (p0) REVERT: E 309 LEU cc_start: 0.8857 (mp) cc_final: 0.8063 (tt) REVERT: E 407 MET cc_start: 0.8104 (mmm) cc_final: 0.7691 (mtp) REVERT: E 425 PHE cc_start: 0.8696 (m-80) cc_final: 0.8439 (m-80) REVERT: E 434 GLN cc_start: 0.8393 (mt0) cc_final: 0.8178 (tm-30) REVERT: E 456 ASP cc_start: 0.8756 (m-30) cc_final: 0.8503 (m-30) REVERT: E 458 LEU cc_start: 0.9274 (mt) cc_final: 0.9032 (tm) REVERT: E 515 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7195 (t0) REVERT: E 522 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9159 (ptmm) outliers start: 63 outliers final: 27 residues processed: 270 average time/residue: 1.1589 time to fit residues: 359.5235 Evaluate side-chains 240 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 542 GLN Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 0.0170 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 0.0670 chunk 188 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN B 542 GLN C 82 GLN D 88 GLN ** E 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18597 Z= 0.184 Angle : 0.578 11.556 25180 Z= 0.293 Chirality : 0.042 0.160 2772 Planarity : 0.004 0.045 3187 Dihedral : 5.188 75.009 2400 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 3.19 % Allowed : 14.50 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.67 (0.18), residues: 2166 helix: 0.64 (0.15), residues: 1302 sheet: -2.26 (0.70), residues: 46 loop : -2.15 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 150 HIS 0.005 0.001 HIS C 189 PHE 0.014 0.001 PHE E 520 TYR 0.026 0.001 TYR E 49 ARG 0.011 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8890 (mt) cc_final: 0.8341 (pp) REVERT: B 36 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7743 (mtm180) REVERT: B 135 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: B 141 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 146 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7850 (mtp180) REVERT: B 279 ASP cc_start: 0.6987 (t0) cc_final: 0.6618 (t0) REVERT: B 291 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6769 (mtm110) REVERT: B 345 TYR cc_start: 0.8132 (t80) cc_final: 0.7845 (t80) REVERT: B 352 ASP cc_start: 0.7968 (t0) cc_final: 0.7575 (t0) REVERT: B 450 SER cc_start: 0.8288 (p) cc_final: 0.7938 (t) REVERT: B 550 LEU cc_start: 0.8501 (tp) cc_final: 0.8226 (mm) REVERT: B 560 LYS cc_start: 0.8333 (mttt) cc_final: 0.7885 (mmmm) REVERT: B 591 ARG cc_start: 0.7535 (ttp-170) cc_final: 0.6944 (ttm110) REVERT: A 11 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8101 (mt-10) REVERT: A 64 ARG cc_start: 0.8662 (ttt180) cc_final: 0.8350 (mtp85) REVERT: A 78 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 119 GLU cc_start: 0.7970 (tt0) cc_final: 0.7550 (tt0) REVERT: A 163 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8253 (mm) REVERT: A 275 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6320 (tptp) REVERT: A 282 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7782 (tttm) REVERT: A 302 SER cc_start: 0.7995 (t) cc_final: 0.7724 (t) REVERT: A 310 ASN cc_start: 0.6838 (t0) cc_final: 0.6461 (m-40) REVERT: A 354 LYS cc_start: 0.8948 (tppt) cc_final: 0.8484 (pttp) REVERT: A 388 LYS cc_start: 0.8461 (tttt) cc_final: 0.8073 (mtmt) REVERT: A 400 THR cc_start: 0.9235 (m) cc_final: 0.9006 (p) REVERT: A 401 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8424 (ptpp) REVERT: A 407 HIS cc_start: 0.8919 (m-70) cc_final: 0.8647 (m-70) REVERT: C 60 ASP cc_start: 0.8145 (t70) cc_final: 0.7121 (t0) REVERT: C 100 MET cc_start: 0.8162 (mmm) cc_final: 0.7945 (mmp) REVERT: C 119 MET cc_start: 0.8779 (ttp) cc_final: 0.8321 (ttp) REVERT: C 120 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8283 (mt-10) REVERT: C 150 LYS cc_start: 0.9003 (mttm) cc_final: 0.8721 (tptt) REVERT: C 226 MET cc_start: 0.8684 (mtm) cc_final: 0.8314 (mtt) REVERT: C 248 ASP cc_start: 0.7897 (m-30) cc_final: 0.7457 (m-30) REVERT: C 270 ASP cc_start: 0.8416 (m-30) cc_final: 0.7905 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7410 (t0) cc_final: 0.6870 (m-30) REVERT: C 300 ASP cc_start: 0.8982 (t70) cc_final: 0.7792 (t0) REVERT: C 342 GLU cc_start: 0.8624 (tp30) cc_final: 0.7768 (tm-30) REVERT: C 368 LYS cc_start: 0.8809 (mttm) cc_final: 0.8558 (ptmm) REVERT: D 17 THR cc_start: 0.9283 (m) cc_final: 0.9032 (t) REVERT: D 19 ASP cc_start: 0.8092 (t0) cc_final: 0.7880 (t0) REVERT: D 20 LYS cc_start: 0.8008 (tttm) cc_final: 0.7655 (tppt) REVERT: D 101 ASN cc_start: 0.7727 (m-40) cc_final: 0.7502 (t0) REVERT: D 104 ASP cc_start: 0.8445 (t0) cc_final: 0.7909 (t0) REVERT: D 117 ASP cc_start: 0.7689 (t0) cc_final: 0.7246 (t70) REVERT: D 162 SER cc_start: 0.8040 (t) cc_final: 0.7800 (p) REVERT: D 165 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: E 35 ASP cc_start: 0.8424 (m-30) cc_final: 0.8037 (m-30) REVERT: E 59 ASN cc_start: 0.8091 (t0) cc_final: 0.7493 (t0) REVERT: E 83 GLU cc_start: 0.8417 (pm20) cc_final: 0.8009 (pm20) REVERT: E 163 ASP cc_start: 0.8719 (m-30) cc_final: 0.8484 (p0) REVERT: E 219 GLN cc_start: 0.7767 (mt0) cc_final: 0.7533 (mt0) REVERT: E 309 LEU cc_start: 0.8826 (mp) cc_final: 0.8081 (tt) REVERT: E 407 MET cc_start: 0.7986 (mmm) cc_final: 0.7596 (mtp) REVERT: E 425 PHE cc_start: 0.8721 (m-80) cc_final: 0.8423 (m-80) REVERT: E 456 ASP cc_start: 0.8778 (m-30) cc_final: 0.8515 (m-30) REVERT: E 458 LEU cc_start: 0.9276 (mt) cc_final: 0.9050 (tm) REVERT: E 515 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7195 (t0) REVERT: E 522 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9101 (ptmm) REVERT: E 538 PRO cc_start: 0.6403 (Cg_endo) cc_final: 0.6199 (Cg_exo) outliers start: 65 outliers final: 26 residues processed: 276 average time/residue: 1.2046 time to fit residues: 381.1341 Evaluate side-chains 233 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 0.5980 chunk 188 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 88 GLN E 283 GLN E 408 ASN E 471 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18597 Z= 0.177 Angle : 0.591 14.506 25180 Z= 0.296 Chirality : 0.041 0.187 2772 Planarity : 0.004 0.046 3187 Dihedral : 5.097 75.104 2400 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 3.44 % Allowed : 15.38 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.47 (0.18), residues: 2166 helix: 0.80 (0.15), residues: 1303 sheet: -2.11 (0.72), residues: 46 loop : -2.07 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 150 HIS 0.005 0.001 HIS C 189 PHE 0.014 0.001 PHE E 468 TYR 0.026 0.001 TYR E 49 ARG 0.012 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 2.095 Fit side-chains revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8935 (mt) cc_final: 0.8310 (pp) REVERT: B 36 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7801 (mtm180) REVERT: B 135 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: B 139 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7012 (mpt-90) REVERT: B 141 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 146 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7829 (mtp180) REVERT: B 150 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8701 (mtmm) REVERT: B 266 ASN cc_start: 0.8024 (t0) cc_final: 0.7773 (t160) REVERT: B 279 ASP cc_start: 0.6911 (t0) cc_final: 0.6484 (t0) REVERT: B 291 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6763 (mtm110) REVERT: B 352 ASP cc_start: 0.7922 (t0) cc_final: 0.7500 (t0) REVERT: B 450 SER cc_start: 0.8220 (p) cc_final: 0.7934 (t) REVERT: B 550 LEU cc_start: 0.8481 (tp) cc_final: 0.8213 (mm) REVERT: B 560 LYS cc_start: 0.8331 (mttt) cc_final: 0.7888 (mmmm) REVERT: B 591 ARG cc_start: 0.7537 (ttp-170) cc_final: 0.6945 (ttm110) REVERT: A 11 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8095 (mt-10) REVERT: A 64 ARG cc_start: 0.8687 (ttt180) cc_final: 0.8377 (mtp85) REVERT: A 78 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 119 GLU cc_start: 0.7920 (tt0) cc_final: 0.7493 (tt0) REVERT: A 163 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 275 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6326 (tptp) REVERT: A 282 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7725 (tttm) REVERT: A 302 SER cc_start: 0.7890 (t) cc_final: 0.7605 (t) REVERT: A 310 ASN cc_start: 0.7029 (t0) cc_final: 0.6584 (m-40) REVERT: A 333 ASN cc_start: 0.8755 (t0) cc_final: 0.7492 (t0) REVERT: A 346 ASP cc_start: 0.7466 (t0) cc_final: 0.7263 (t0) REVERT: A 354 LYS cc_start: 0.8910 (tppt) cc_final: 0.8493 (pttp) REVERT: A 388 LYS cc_start: 0.8416 (tttt) cc_final: 0.7969 (mtmt) REVERT: A 396 ASP cc_start: 0.7096 (p0) cc_final: 0.6492 (p0) REVERT: A 400 THR cc_start: 0.9220 (m) cc_final: 0.8985 (p) REVERT: A 401 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8462 (ptpp) REVERT: C 60 ASP cc_start: 0.8144 (t70) cc_final: 0.7134 (t0) REVERT: C 100 MET cc_start: 0.8123 (mmm) cc_final: 0.7905 (mmp) REVERT: C 119 MET cc_start: 0.8779 (ttp) cc_final: 0.8305 (ttp) REVERT: C 150 LYS cc_start: 0.9009 (mttm) cc_final: 0.8723 (tptt) REVERT: C 226 MET cc_start: 0.8664 (mtm) cc_final: 0.8435 (mtt) REVERT: C 230 ASP cc_start: 0.8806 (t0) cc_final: 0.8274 (t0) REVERT: C 248 ASP cc_start: 0.7894 (m-30) cc_final: 0.7444 (m-30) REVERT: C 270 ASP cc_start: 0.8413 (m-30) cc_final: 0.7847 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7417 (t0) cc_final: 0.6868 (m-30) REVERT: C 295 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7719 (mmt90) REVERT: C 300 ASP cc_start: 0.8839 (t70) cc_final: 0.8270 (t0) REVERT: C 342 GLU cc_start: 0.8576 (tp30) cc_final: 0.7746 (tm-30) REVERT: C 368 LYS cc_start: 0.8821 (mttm) cc_final: 0.8573 (ptmm) REVERT: D 17 THR cc_start: 0.9259 (m) cc_final: 0.8990 (t) REVERT: D 21 LYS cc_start: 0.8615 (tmmm) cc_final: 0.8264 (tmmt) REVERT: D 24 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7148 (tm-30) REVERT: D 101 ASN cc_start: 0.7690 (m-40) cc_final: 0.7483 (t0) REVERT: D 104 ASP cc_start: 0.8452 (t0) cc_final: 0.7961 (t0) REVERT: D 117 ASP cc_start: 0.7687 (t0) cc_final: 0.7236 (t70) REVERT: D 162 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7880 (p) REVERT: D 165 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: E 35 ASP cc_start: 0.8386 (m-30) cc_final: 0.8051 (m-30) REVERT: E 59 ASN cc_start: 0.8078 (t0) cc_final: 0.7523 (t0) REVERT: E 83 GLU cc_start: 0.8369 (pm20) cc_final: 0.7886 (pm20) REVERT: E 163 ASP cc_start: 0.8741 (m-30) cc_final: 0.8494 (p0) REVERT: E 222 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7809 (p) REVERT: E 309 LEU cc_start: 0.8795 (mp) cc_final: 0.8070 (tt) REVERT: E 354 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7873 (tmtt) REVERT: E 407 MET cc_start: 0.7962 (mmm) cc_final: 0.7581 (mtp) REVERT: E 425 PHE cc_start: 0.8719 (m-80) cc_final: 0.8413 (m-80) REVERT: E 456 ASP cc_start: 0.8748 (m-30) cc_final: 0.8465 (m-30) REVERT: E 458 LEU cc_start: 0.9285 (mt) cc_final: 0.9050 (tm) REVERT: E 515 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7171 (t0) REVERT: E 522 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9074 (ptmm) outliers start: 70 outliers final: 27 residues processed: 270 average time/residue: 1.1505 time to fit residues: 354.4975 Evaluate side-chains 238 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 277 THR 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 433 SER 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 129 SER Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 209 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN B 542 GLN C 82 GLN C 222 GLN C 303 GLN D 88 GLN E 434 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18597 Z= 0.191 Angle : 0.597 14.062 25180 Z= 0.298 Chirality : 0.042 0.168 2772 Planarity : 0.004 0.051 3187 Dihedral : 5.062 74.953 2400 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 2.85 % Allowed : 16.27 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.31 (0.18), residues: 2166 helix: 0.94 (0.15), residues: 1296 sheet: -1.97 (0.73), residues: 46 loop : -2.01 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 150 HIS 0.005 0.001 HIS C 189 PHE 0.013 0.001 PHE B 415 TYR 0.025 0.001 TYR E 49 ARG 0.012 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 2.230 Fit side-chains revert: symmetry clash REVERT: B 36 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7815 (mtm180) REVERT: B 135 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: B 141 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 146 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7829 (mtp180) REVERT: B 150 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8669 (tppp) REVERT: B 279 ASP cc_start: 0.6970 (t0) cc_final: 0.6547 (t0) REVERT: B 291 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6753 (mtm110) REVERT: B 352 ASP cc_start: 0.7924 (t0) cc_final: 0.7500 (t0) REVERT: B 385 ASP cc_start: 0.7694 (t0) cc_final: 0.7369 (m-30) REVERT: B 450 SER cc_start: 0.8177 (p) cc_final: 0.7934 (t) REVERT: B 542 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: B 550 LEU cc_start: 0.8492 (tp) cc_final: 0.8229 (mm) REVERT: B 560 LYS cc_start: 0.8306 (mttt) cc_final: 0.7881 (mmmm) REVERT: A 64 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8379 (mtp85) REVERT: A 78 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 119 GLU cc_start: 0.7977 (tt0) cc_final: 0.7572 (tt0) REVERT: A 163 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 275 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6383 (tptm) REVERT: A 282 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7778 (tttm) REVERT: A 302 SER cc_start: 0.7854 (t) cc_final: 0.7568 (t) REVERT: A 310 ASN cc_start: 0.7086 (t0) cc_final: 0.6724 (m-40) REVERT: A 354 LYS cc_start: 0.8879 (tppt) cc_final: 0.8477 (pttp) REVERT: A 388 LYS cc_start: 0.8472 (tttt) cc_final: 0.8037 (mtmt) REVERT: A 396 ASP cc_start: 0.7279 (p0) cc_final: 0.6630 (p0) REVERT: A 400 THR cc_start: 0.9204 (m) cc_final: 0.8934 (p) REVERT: A 401 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8468 (ptpp) REVERT: C 60 ASP cc_start: 0.8144 (t70) cc_final: 0.7133 (t0) REVERT: C 100 MET cc_start: 0.8125 (mmm) cc_final: 0.7908 (mmp) REVERT: C 119 MET cc_start: 0.8769 (ttp) cc_final: 0.8309 (ttp) REVERT: C 150 LYS cc_start: 0.9015 (mttm) cc_final: 0.8730 (tptt) REVERT: C 226 MET cc_start: 0.8661 (mtm) cc_final: 0.8439 (mtt) REVERT: C 248 ASP cc_start: 0.7907 (m-30) cc_final: 0.7453 (m-30) REVERT: C 270 ASP cc_start: 0.8416 (m-30) cc_final: 0.7841 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7465 (t0) cc_final: 0.6911 (m-30) REVERT: C 295 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7744 (mmt90) REVERT: C 300 ASP cc_start: 0.8599 (t70) cc_final: 0.8193 (t0) REVERT: C 368 LYS cc_start: 0.8815 (mttm) cc_final: 0.8569 (ptmm) REVERT: D 17 THR cc_start: 0.9233 (m) cc_final: 0.8931 (t) REVERT: D 19 ASP cc_start: 0.7999 (t0) cc_final: 0.7773 (t0) REVERT: D 21 LYS cc_start: 0.8510 (tmmm) cc_final: 0.8202 (tmmm) REVERT: D 24 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7121 (tm-30) REVERT: D 89 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7851 (mmmt) REVERT: D 101 ASN cc_start: 0.7722 (m-40) cc_final: 0.7512 (t0) REVERT: D 104 ASP cc_start: 0.8419 (t0) cc_final: 0.7934 (t0) REVERT: D 117 ASP cc_start: 0.7637 (t0) cc_final: 0.7172 (t70) REVERT: D 162 SER cc_start: 0.8115 (OUTLIER) cc_final: 0.7884 (p) REVERT: D 165 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: E 35 ASP cc_start: 0.8369 (m-30) cc_final: 0.8043 (m-30) REVERT: E 59 ASN cc_start: 0.7989 (t0) cc_final: 0.7413 (t0) REVERT: E 83 GLU cc_start: 0.8341 (pm20) cc_final: 0.7843 (pm20) REVERT: E 163 ASP cc_start: 0.8738 (m-30) cc_final: 0.8454 (p0) REVERT: E 309 LEU cc_start: 0.8809 (mp) cc_final: 0.8109 (tt) REVERT: E 407 MET cc_start: 0.7819 (mmm) cc_final: 0.7420 (mtp) REVERT: E 425 PHE cc_start: 0.8791 (m-80) cc_final: 0.8474 (m-80) REVERT: E 458 LEU cc_start: 0.9287 (mt) cc_final: 0.9066 (tm) REVERT: E 515 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7225 (t0) REVERT: E 522 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9049 (ptmm) outliers start: 58 outliers final: 30 residues processed: 251 average time/residue: 1.1380 time to fit residues: 327.2262 Evaluate side-chains 235 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 542 GLN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 277 THR 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 380 LEU Chi-restraints excluded: chain A residue 433 SER 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 129 SER Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 0.0770 chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 103 optimal weight: 0.0060 chunk 19 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18597 Z= 0.156 Angle : 0.596 14.174 25180 Z= 0.295 Chirality : 0.041 0.170 2772 Planarity : 0.004 0.054 3187 Dihedral : 5.000 75.293 2400 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 2.70 % Allowed : 16.86 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.18 (0.18), residues: 2166 helix: 0.99 (0.15), residues: 1309 sheet: -1.89 (0.65), residues: 56 loop : -1.89 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 150 HIS 0.004 0.001 HIS C 189 PHE 0.016 0.001 PHE E 468 TYR 0.026 0.001 TYR E 49 ARG 0.013 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7748 (mt0) REVERT: B 36 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7534 (mtm180) REVERT: B 135 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: B 139 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7002 (mpt-90) REVERT: B 141 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8318 (mm-30) REVERT: B 146 ARG cc_start: 0.8064 (ttp-110) cc_final: 0.7835 (mtp180) REVERT: B 150 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8663 (tppp) REVERT: B 266 ASN cc_start: 0.7952 (t0) cc_final: 0.7691 (t160) REVERT: B 279 ASP cc_start: 0.6933 (t0) cc_final: 0.6522 (t0) REVERT: B 291 ARG cc_start: 0.7127 (mtt180) cc_final: 0.6737 (mtm110) REVERT: B 352 ASP cc_start: 0.7982 (t0) cc_final: 0.7547 (t0) REVERT: B 385 ASP cc_start: 0.7708 (t0) cc_final: 0.7381 (m-30) REVERT: B 550 LEU cc_start: 0.8482 (tp) cc_final: 0.8184 (mm) REVERT: B 560 LYS cc_start: 0.8305 (mttt) cc_final: 0.7881 (mmmm) REVERT: A 64 ARG cc_start: 0.8684 (ttt180) cc_final: 0.8372 (mtp85) REVERT: A 78 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 119 GLU cc_start: 0.7917 (tt0) cc_final: 0.7649 (tt0) REVERT: A 163 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8242 (mm) REVERT: A 275 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6395 (tptm) REVERT: A 282 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7757 (tttm) REVERT: A 302 SER cc_start: 0.7887 (t) cc_final: 0.7598 (t) REVERT: A 310 ASN cc_start: 0.7070 (t0) cc_final: 0.6755 (m-40) REVERT: A 333 ASN cc_start: 0.8779 (t0) cc_final: 0.7458 (t0) REVERT: A 354 LYS cc_start: 0.8837 (tppt) cc_final: 0.8472 (pttp) REVERT: A 388 LYS cc_start: 0.8447 (tttt) cc_final: 0.8030 (mtmt) REVERT: A 396 ASP cc_start: 0.7228 (p0) cc_final: 0.6593 (p0) REVERT: A 400 THR cc_start: 0.9069 (m) cc_final: 0.8766 (p) REVERT: A 401 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8467 (ptpp) REVERT: A 412 GLU cc_start: 0.6941 (tt0) cc_final: 0.6614 (pt0) REVERT: C 60 ASP cc_start: 0.8040 (t70) cc_final: 0.7095 (t0) REVERT: C 100 MET cc_start: 0.8112 (mmm) cc_final: 0.7898 (mmp) REVERT: C 119 MET cc_start: 0.8784 (ttp) cc_final: 0.8301 (ttp) REVERT: C 150 LYS cc_start: 0.9001 (mttm) cc_final: 0.8712 (tptt) REVERT: C 230 ASP cc_start: 0.8805 (t0) cc_final: 0.8260 (t0) REVERT: C 248 ASP cc_start: 0.7903 (m-30) cc_final: 0.7455 (m-30) REVERT: C 270 ASP cc_start: 0.8419 (m-30) cc_final: 0.7851 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7459 (t0) cc_final: 0.6902 (m-30) REVERT: C 295 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7768 (mmt90) REVERT: C 300 ASP cc_start: 0.8520 (t70) cc_final: 0.8091 (t0) REVERT: C 368 LYS cc_start: 0.8816 (mttm) cc_final: 0.8552 (ptmm) REVERT: D 17 THR cc_start: 0.9210 (m) cc_final: 0.8897 (t) REVERT: D 21 LYS cc_start: 0.8618 (tmmm) cc_final: 0.8289 (tmmt) REVERT: D 24 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7086 (tm-30) REVERT: D 101 ASN cc_start: 0.7665 (m-40) cc_final: 0.7447 (t0) REVERT: D 104 ASP cc_start: 0.8375 (t0) cc_final: 0.7935 (t0) REVERT: D 117 ASP cc_start: 0.7569 (t0) cc_final: 0.7126 (t70) REVERT: D 162 SER cc_start: 0.8113 (t) cc_final: 0.7904 (p) REVERT: D 165 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: E 35 ASP cc_start: 0.8401 (m-30) cc_final: 0.8062 (m-30) REVERT: E 59 ASN cc_start: 0.8060 (t0) cc_final: 0.7497 (t0) REVERT: E 83 GLU cc_start: 0.8329 (pm20) cc_final: 0.7822 (pm20) REVERT: E 163 ASP cc_start: 0.8781 (m-30) cc_final: 0.8545 (p0) REVERT: E 309 LEU cc_start: 0.8821 (mp) cc_final: 0.8150 (tt) REVERT: E 407 MET cc_start: 0.7842 (mmm) cc_final: 0.7523 (mtp) REVERT: E 425 PHE cc_start: 0.8787 (m-80) cc_final: 0.8445 (m-80) REVERT: E 515 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7288 (t0) REVERT: E 522 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (ptmm) outliers start: 55 outliers final: 29 residues processed: 254 average time/residue: 1.1426 time to fit residues: 332.2310 Evaluate side-chains 239 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 277 THR 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 380 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 440 ILE 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 129 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 474 GLN A 439 HIS C 82 GLN C 235 GLN E 86 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18597 Z= 0.302 Angle : 0.662 13.438 25180 Z= 0.328 Chirality : 0.044 0.222 2772 Planarity : 0.004 0.061 3187 Dihedral : 5.104 73.980 2400 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 2.65 % Allowed : 17.54 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.29 (0.18), residues: 2166 helix: 0.92 (0.15), residues: 1305 sheet: -1.75 (0.77), residues: 46 loop : -1.97 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 150 HIS 0.005 0.001 HIS A 439 PHE 0.021 0.002 PHE B 2 TYR 0.024 0.002 TYR C 237 ARG 0.013 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7799 (mt0) REVERT: B 36 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7656 (mtm180) REVERT: B 95 ASP cc_start: 0.7874 (p0) cc_final: 0.7628 (t0) REVERT: B 135 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: B 141 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8362 (mm-30) REVERT: B 146 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7808 (mtm-85) REVERT: B 150 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8629 (tppp) REVERT: B 279 ASP cc_start: 0.6936 (t0) cc_final: 0.6532 (t0) REVERT: B 291 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6751 (mtm110) REVERT: B 352 ASP cc_start: 0.7840 (t0) cc_final: 0.7402 (t0) REVERT: B 385 ASP cc_start: 0.7850 (t0) cc_final: 0.7494 (m-30) REVERT: B 560 LYS cc_start: 0.8305 (mttt) cc_final: 0.7928 (mmmt) REVERT: A 64 ARG cc_start: 0.8670 (ttt180) cc_final: 0.8398 (mtp85) REVERT: A 66 MET cc_start: 0.8404 (mtp) cc_final: 0.7950 (ttm) REVERT: A 78 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 119 GLU cc_start: 0.7951 (tt0) cc_final: 0.7389 (tt0) REVERT: A 163 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8103 (mm) REVERT: A 275 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6371 (tptm) REVERT: A 282 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7884 (tttm) REVERT: A 302 SER cc_start: 0.7803 (t) cc_final: 0.7367 (t) REVERT: A 310 ASN cc_start: 0.7294 (t0) cc_final: 0.6933 (m-40) REVERT: A 354 LYS cc_start: 0.8900 (tppt) cc_final: 0.8474 (pttp) REVERT: A 388 LYS cc_start: 0.8480 (tttt) cc_final: 0.8044 (mtmt) REVERT: A 396 ASP cc_start: 0.7369 (p0) cc_final: 0.6630 (p0) REVERT: A 400 THR cc_start: 0.9172 (m) cc_final: 0.8930 (p) REVERT: A 401 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8463 (ptpp) REVERT: A 412 GLU cc_start: 0.7028 (tt0) cc_final: 0.6755 (tt0) REVERT: C 60 ASP cc_start: 0.8169 (t70) cc_final: 0.7139 (t0) REVERT: C 100 MET cc_start: 0.8155 (mmm) cc_final: 0.7934 (mmp) REVERT: C 119 MET cc_start: 0.8780 (ttp) cc_final: 0.8312 (ttp) REVERT: C 150 LYS cc_start: 0.9029 (mttm) cc_final: 0.8738 (tptt) REVERT: C 248 ASP cc_start: 0.7954 (m-30) cc_final: 0.7530 (m-30) REVERT: C 270 ASP cc_start: 0.8426 (m-30) cc_final: 0.7838 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7483 (t0) cc_final: 0.6960 (m-30) REVERT: C 300 ASP cc_start: 0.8650 (t70) cc_final: 0.8217 (t0) REVERT: C 368 LYS cc_start: 0.8830 (mttm) cc_final: 0.8592 (ptmm) REVERT: D 17 THR cc_start: 0.9259 (m) cc_final: 0.8943 (t) REVERT: D 21 LYS cc_start: 0.8693 (tmmm) cc_final: 0.8351 (tmmm) REVERT: D 24 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7188 (tm-30) REVERT: D 75 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7736 (pp) REVERT: D 101 ASN cc_start: 0.7979 (m-40) cc_final: 0.7747 (t0) REVERT: D 104 ASP cc_start: 0.8468 (t0) cc_final: 0.7926 (t0) REVERT: D 117 ASP cc_start: 0.7635 (t0) cc_final: 0.7144 (t70) REVERT: D 162 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7905 (p) REVERT: D 165 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: E 35 ASP cc_start: 0.8356 (m-30) cc_final: 0.8025 (m-30) REVERT: E 59 ASN cc_start: 0.7966 (t0) cc_final: 0.7423 (t0) REVERT: E 83 GLU cc_start: 0.8372 (pm20) cc_final: 0.7820 (pm20) REVERT: E 146 ILE cc_start: 0.8348 (mm) cc_final: 0.8134 (mm) REVERT: E 163 ASP cc_start: 0.8770 (m-30) cc_final: 0.8495 (p0) REVERT: E 309 LEU cc_start: 0.8891 (mp) cc_final: 0.8212 (tt) REVERT: E 425 PHE cc_start: 0.8819 (m-80) cc_final: 0.8488 (m-80) REVERT: E 515 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7322 (t0) REVERT: E 522 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8997 (ptmm) outliers start: 54 outliers final: 26 residues processed: 245 average time/residue: 1.0994 time to fit residues: 310.0563 Evaluate side-chains 228 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 277 THR 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 380 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 ASN C 82 GLN C 235 GLN E 434 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18597 Z= 0.188 Angle : 0.633 13.648 25180 Z= 0.312 Chirality : 0.043 0.223 2772 Planarity : 0.004 0.061 3187 Dihedral : 5.072 74.508 2400 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 2.06 % Allowed : 18.67 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.14 (0.18), residues: 2166 helix: 1.03 (0.15), residues: 1305 sheet: -1.74 (0.67), residues: 56 loop : -1.89 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 150 HIS 0.004 0.001 HIS C 189 PHE 0.013 0.001 PHE B 2 TYR 0.026 0.001 TYR E 49 ARG 0.014 0.000 ARG A 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7812 (mt0) REVERT: B 36 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7707 (mtm180) REVERT: B 95 ASP cc_start: 0.7892 (p0) cc_final: 0.7628 (t0) REVERT: B 135 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: B 146 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7811 (mtp180) REVERT: B 150 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8640 (tppp) REVERT: B 279 ASP cc_start: 0.6954 (t0) cc_final: 0.6567 (t0) REVERT: B 291 ARG cc_start: 0.7192 (mtt180) cc_final: 0.6744 (mtm110) REVERT: B 352 ASP cc_start: 0.7813 (t0) cc_final: 0.7386 (t0) REVERT: B 385 ASP cc_start: 0.7821 (t0) cc_final: 0.7456 (m-30) REVERT: B 550 LEU cc_start: 0.8588 (tp) cc_final: 0.8291 (mm) REVERT: B 560 LYS cc_start: 0.8301 (mttt) cc_final: 0.7924 (mmmt) REVERT: A 64 ARG cc_start: 0.8668 (ttt180) cc_final: 0.8395 (mtp85) REVERT: A 66 MET cc_start: 0.8407 (mtp) cc_final: 0.7967 (ttm) REVERT: A 78 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7754 (mm-30) REVERT: A 119 GLU cc_start: 0.7820 (tt0) cc_final: 0.7443 (tt0) REVERT: A 163 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7973 (mm) REVERT: A 275 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6360 (tptm) REVERT: A 282 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7826 (tttm) REVERT: A 302 SER cc_start: 0.8022 (t) cc_final: 0.7529 (p) REVERT: A 310 ASN cc_start: 0.7199 (t0) cc_final: 0.6828 (m-40) REVERT: A 333 ASN cc_start: 0.8747 (t0) cc_final: 0.7395 (t0) REVERT: A 354 LYS cc_start: 0.8836 (tppt) cc_final: 0.8470 (pttp) REVERT: A 388 LYS cc_start: 0.8456 (tttt) cc_final: 0.8026 (mtmt) REVERT: A 396 ASP cc_start: 0.7307 (p0) cc_final: 0.6531 (p0) REVERT: A 400 THR cc_start: 0.9079 (m) cc_final: 0.8761 (p) REVERT: A 401 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8445 (ptpp) REVERT: A 412 GLU cc_start: 0.6975 (tt0) cc_final: 0.6436 (pt0) REVERT: C 60 ASP cc_start: 0.8036 (t70) cc_final: 0.7035 (t0) REVERT: C 100 MET cc_start: 0.8157 (mmm) cc_final: 0.7939 (mmp) REVERT: C 119 MET cc_start: 0.8761 (ttp) cc_final: 0.8290 (ttp) REVERT: C 150 LYS cc_start: 0.9023 (mttm) cc_final: 0.8733 (tptt) REVERT: C 248 ASP cc_start: 0.7915 (m-30) cc_final: 0.7492 (m-30) REVERT: C 270 ASP cc_start: 0.8418 (m-30) cc_final: 0.7848 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7499 (t0) cc_final: 0.6990 (m-30) REVERT: C 342 GLU cc_start: 0.8592 (tp30) cc_final: 0.7809 (tm-30) REVERT: C 368 LYS cc_start: 0.8820 (mttm) cc_final: 0.8547 (ptmm) REVERT: D 17 THR cc_start: 0.9222 (m) cc_final: 0.8915 (t) REVERT: D 21 LYS cc_start: 0.8571 (tmmm) cc_final: 0.8277 (tmmm) REVERT: D 24 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7147 (tm-30) REVERT: D 75 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7758 (pp) REVERT: D 101 ASN cc_start: 0.7770 (m-40) cc_final: 0.7549 (t0) REVERT: D 104 ASP cc_start: 0.8342 (t0) cc_final: 0.7869 (t0) REVERT: D 117 ASP cc_start: 0.7564 (t0) cc_final: 0.7066 (t70) REVERT: D 165 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: E 35 ASP cc_start: 0.8380 (m-30) cc_final: 0.8047 (m-30) REVERT: E 59 ASN cc_start: 0.7938 (t0) cc_final: 0.7396 (t0) REVERT: E 83 GLU cc_start: 0.8370 (pm20) cc_final: 0.7807 (pm20) REVERT: E 163 ASP cc_start: 0.8747 (m-30) cc_final: 0.8461 (p0) REVERT: E 309 LEU cc_start: 0.8866 (mp) cc_final: 0.8262 (tt) REVERT: E 407 MET cc_start: 0.7886 (mmm) cc_final: 0.7499 (mtp) REVERT: E 425 PHE cc_start: 0.8802 (m-80) cc_final: 0.8467 (m-80) REVERT: E 515 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7400 (t0) REVERT: E 522 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8970 (ptmm) outliers start: 42 outliers final: 24 residues processed: 234 average time/residue: 1.1076 time to fit residues: 298.9270 Evaluate side-chains 234 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 277 THR 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 380 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN C 82 GLN C 235 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087823 restraints weight = 28712.470| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.56 r_work: 0.2965 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4175 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: