Starting phenix.real_space_refine on Mon Jun 16 04:13:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gyu_0097/06_2025/6gyu_0097.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gyu_0097/06_2025/6gyu_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/cci-nas-00/data/ceres_data/6gyu_0097/06_2025/6gyu_0097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gyu_0097/06_2025/6gyu_0097.map" model { file = "/net/cci-nas-00/data/ceres_data/6gyu_0097/06_2025/6gyu_0097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gyu_0097/06_2025/6gyu_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.55, per 1000 atoms: 0.53 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: 4.05 Conformation dependent library (CDL) restraints added in 2.1 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: 1.69 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: 4.76 Time building geometry restraints manager: 4.85 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.380 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.270 ------------------------------------------------------------------------------- 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 : 0.006 0.217 18606 Z= 0.264 Angle : 0.976 18.431 25194 Z= 0.524 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 Details of bonding type rmsd hydrogen bonds : bond 0.16184 ( 835) hydrogen bonds : angle 6.73519 ( 2451) metal coordination : bond 0.17631 ( 8) metal coordination : angle 12.32055 ( 12) SS BOND : bond 0.00111 ( 1) SS BOND : angle 3.42475 ( 2) covalent geometry : bond 0.00516 (18597) covalent geometry : angle 0.93748 (25180) *********************** 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 : 2.078 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: 1.3644 time to fit residues: 770.4186 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 : 2.342 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092103 restraints weight = 28928.623| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.81 r_work: 0.3033 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 18606 Z= 0.152 Angle : 0.669 15.303 25194 Z= 0.338 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 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 835) hydrogen bonds : angle 4.63716 ( 2451) metal coordination : bond 0.00639 ( 8) metal coordination : angle 7.67441 ( 12) SS BOND : bond 0.00097 ( 1) SS BOND : angle 2.40931 ( 2) covalent geometry : bond 0.00348 (18597) covalent geometry : angle 0.64713 (25180) *********************** 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 : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.9007 (mt) cc_final: 0.8618 (pp) REVERT: B 97 GLU cc_start: 0.8439 (pt0) cc_final: 0.8159 (tp30) REVERT: B 146 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8147 (mtm-85) REVERT: B 291 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7976 (mtm110) REVERT: B 345 TYR cc_start: 0.8436 (t80) cc_final: 0.8181 (t80) REVERT: B 354 ASP cc_start: 0.8905 (m-30) cc_final: 0.8674 (m-30) REVERT: B 423 ASP cc_start: 0.8273 (t0) cc_final: 0.8000 (t0) REVERT: B 461 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8638 (mm110) REVERT: B 550 LEU cc_start: 0.8985 (tp) cc_final: 0.8752 (mm) REVERT: B 560 LYS cc_start: 0.8858 (mttt) cc_final: 0.8390 (mmmm) REVERT: A 36 ILE cc_start: 0.7420 (mp) cc_final: 0.7211 (mm) REVERT: A 78 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8347 (mm-30) REVERT: A 119 GLU cc_start: 0.8426 (tt0) cc_final: 0.8084 (tt0) REVERT: A 275 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7453 (tptm) REVERT: A 282 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7880 (tmtp) REVERT: A 310 ASN cc_start: 0.7442 (t0) cc_final: 0.7168 (m-40) REVERT: A 336 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8365 (mttm) REVERT: A 354 LYS cc_start: 0.9086 (tppt) cc_final: 0.8828 (tmmt) REVERT: A 394 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8110 (tm-30) REVERT: A 401 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8707 (ptpp) REVERT: C 60 ASP cc_start: 0.8624 (t70) cc_final: 0.7810 (t0) REVERT: C 185 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8134 (t) REVERT: C 248 ASP cc_start: 0.8250 (m-30) cc_final: 0.7950 (m-30) REVERT: C 270 ASP cc_start: 0.8612 (m-30) cc_final: 0.8196 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7654 (t0) cc_final: 0.7176 (m-30) REVERT: C 295 ARG cc_start: 0.8764 (mmt90) cc_final: 0.8466 (mmm160) REVERT: C 300 ASP cc_start: 0.9213 (t0) cc_final: 0.8881 (t0) REVERT: C 342 GLU cc_start: 0.8531 (tp30) cc_final: 0.7846 (tm-30) REVERT: C 387 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9180 (mp) REVERT: D 20 LYS cc_start: 0.8740 (tttm) cc_final: 0.8234 (tttt) REVERT: D 98 ARG cc_start: 0.9077 (ttp-110) cc_final: 0.8789 (ttm110) REVERT: D 104 ASP cc_start: 0.8459 (t0) cc_final: 0.8110 (t0) REVERT: D 117 ASP cc_start: 0.8326 (t0) cc_final: 0.7945 (t70) REVERT: E 31 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7170 (tp40) REVERT: E 35 ASP cc_start: 0.8544 (m-30) cc_final: 0.8046 (m-30) REVERT: E 59 ASN cc_start: 0.8682 (t0) cc_final: 0.8333 (t0) REVERT: E 309 LEU cc_start: 0.8875 (mp) cc_final: 0.7847 (tt) REVERT: E 329 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8426 (tm) REVERT: E 336 GLU cc_start: 0.8323 (pm20) cc_final: 0.8003 (tp30) REVERT: E 407 MET cc_start: 0.8062 (mtp) cc_final: 0.7697 (mtt) REVERT: E 434 GLN cc_start: 0.8390 (mt0) cc_final: 0.8015 (tm-30) REVERT: E 456 ASP cc_start: 0.8696 (m-30) cc_final: 0.8347 (m-30) REVERT: E 468 PHE cc_start: 0.8704 (t80) cc_final: 0.8022 (t80) REVERT: E 479 PHE cc_start: 0.8437 (m-80) cc_final: 0.8080 (m-10) outliers start: 61 outliers final: 18 residues processed: 335 average time/residue: 1.2374 time to fit residues: 468.0079 Evaluate side-chains 239 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 119 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 198 optimal weight: 0.0870 chunk 175 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN B 474 GLN A 27 ASN A 171 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.129976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088453 restraints weight = 28742.295| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.56 r_work: 0.2988 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18606 Z= 0.174 Angle : 0.649 12.764 25194 Z= 0.327 Chirality : 0.043 0.173 2772 Planarity : 0.004 0.049 3187 Dihedral : 5.558 74.367 2400 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 3.59 % Allowed : 13.17 % Favored : 83.24 % 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: -1.50 (0.17), residues: 2166 helix: -0.04 (0.14), residues: 1308 sheet: -2.75 (0.63), residues: 46 loop : -2.46 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 150 HIS 0.014 0.001 HIS E 445 PHE 0.020 0.002 PHE E 468 TYR 0.029 0.002 TYR E 49 ARG 0.009 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 835) hydrogen bonds : angle 4.30512 ( 2451) metal coordination : bond 0.00432 ( 8) metal coordination : angle 6.96872 ( 12) SS BOND : bond 0.00275 ( 1) SS BOND : angle 1.36250 ( 2) covalent geometry : bond 0.00410 (18597) covalent geometry : angle 0.63094 (25180) *********************** 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 295 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 222 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8951 (mt) cc_final: 0.8505 (pp) REVERT: B 19 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7919 (ptp-110) REVERT: B 43 MET cc_start: 0.8065 (mmm) cc_final: 0.7486 (mmm) REVERT: B 97 GLU cc_start: 0.8558 (pt0) cc_final: 0.8284 (tp30) REVERT: B 135 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: B 291 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8112 (mtm110) REVERT: B 423 ASP cc_start: 0.8441 (t0) cc_final: 0.8175 (t0) REVERT: B 461 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8776 (mm110) REVERT: B 550 LEU cc_start: 0.9155 (tp) cc_final: 0.8908 (mm) REVERT: B 560 LYS cc_start: 0.8836 (mttt) cc_final: 0.8319 (mmmm) REVERT: A 46 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8681 (mm-30) REVERT: A 66 MET cc_start: 0.8868 (mtp) cc_final: 0.8656 (mtp) REVERT: A 78 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8568 (mm-30) REVERT: A 119 GLU cc_start: 0.8665 (tt0) cc_final: 0.8364 (tt0) REVERT: A 163 LEU cc_start: 0.8976 (mm) cc_final: 0.8770 (mm) REVERT: A 175 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7465 (pp) REVERT: A 183 CYS cc_start: 0.8917 (t) cc_final: 0.8686 (m) REVERT: A 275 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7537 (tptm) REVERT: A 310 ASN cc_start: 0.7860 (t0) cc_final: 0.7453 (m-40) REVERT: A 354 LYS cc_start: 0.9184 (tppt) cc_final: 0.8791 (pttt) REVERT: A 401 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8773 (ptpp) REVERT: C 60 ASP cc_start: 0.8813 (t70) cc_final: 0.7963 (t0) REVERT: C 100 MET cc_start: 0.8634 (mmm) cc_final: 0.8326 (mmp) REVERT: C 119 MET cc_start: 0.9351 (ttp) cc_final: 0.8983 (ttp) REVERT: C 226 MET cc_start: 0.9112 (mtm) cc_final: 0.8843 (mtt) REVERT: C 248 ASP cc_start: 0.8566 (m-30) cc_final: 0.8285 (m-30) REVERT: C 270 ASP cc_start: 0.8789 (m-30) cc_final: 0.8301 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7618 (t0) cc_final: 0.7032 (m-30) REVERT: C 295 ARG cc_start: 0.9060 (mmt90) cc_final: 0.8670 (mmm-85) REVERT: C 300 ASP cc_start: 0.9393 (t0) cc_final: 0.8845 (t0) REVERT: C 342 GLU cc_start: 0.8651 (tp30) cc_final: 0.7940 (tm-30) REVERT: D 20 LYS cc_start: 0.8782 (tttm) cc_final: 0.8326 (tppt) REVERT: D 104 ASP cc_start: 0.8606 (t0) cc_final: 0.8226 (t0) REVERT: D 106 ASP cc_start: 0.8660 (m-30) cc_final: 0.8455 (m-30) REVERT: D 117 ASP cc_start: 0.8344 (t0) cc_final: 0.7995 (t70) REVERT: E 35 ASP cc_start: 0.8690 (m-30) cc_final: 0.8315 (m-30) REVERT: E 59 ASN cc_start: 0.8690 (t0) cc_final: 0.8270 (t0) REVERT: E 83 GLU cc_start: 0.8819 (pm20) cc_final: 0.8485 (pm20) REVERT: E 309 LEU cc_start: 0.8843 (mp) cc_final: 0.7842 (tt) REVERT: E 425 PHE cc_start: 0.8592 (m-80) cc_final: 0.8343 (m-80) REVERT: E 434 GLN cc_start: 0.8428 (mt0) cc_final: 0.8099 (tm-30) REVERT: E 456 ASP cc_start: 0.8624 (m-30) cc_final: 0.8370 (m-30) REVERT: E 468 PHE cc_start: 0.8779 (t80) cc_final: 0.8452 (t80) REVERT: E 479 PHE cc_start: 0.8430 (m-80) cc_final: 0.7938 (m-80) REVERT: E 522 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9169 (ptmm) outliers start: 73 outliers final: 29 residues processed: 271 average time/residue: 1.2065 time to fit residues: 370.2269 Evaluate side-chains 229 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 91 ASN 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 46 GLU 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 179 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 A residue 478 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 460 MET 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 166 ILE 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 42 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 193 optimal weight: 30.0000 chunk 129 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 ASN A 27 ASN C 82 GLN C 552 ASN D 34 ASN E 266 HIS ** E 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.088733 restraints weight = 28713.615| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.89 r_work: 0.2960 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18606 Z= 0.160 Angle : 0.619 12.291 25194 Z= 0.311 Chirality : 0.043 0.171 2772 Planarity : 0.004 0.049 3187 Dihedral : 5.419 74.314 2400 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 3.83 % Allowed : 13.91 % Favored : 82.26 % 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: -1.03 (0.18), residues: 2166 helix: 0.37 (0.15), residues: 1294 sheet: -2.54 (0.65), residues: 46 loop : -2.29 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 150 HIS 0.006 0.001 HIS C 189 PHE 0.022 0.002 PHE E 468 TYR 0.027 0.001 TYR E 49 ARG 0.009 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 835) hydrogen bonds : angle 4.13372 ( 2451) metal coordination : bond 0.00391 ( 8) metal coordination : angle 6.61795 ( 12) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.28370 ( 2) covalent geometry : bond 0.00379 (18597) covalent geometry : angle 0.60181 (25180) *********************** 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: 78 poor density : 210 time to evaluate : 2.060 Fit side-chains revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8982 (mt) cc_final: 0.8546 (pp) REVERT: B 43 MET cc_start: 0.8064 (mmm) cc_final: 0.7699 (mmm) REVERT: B 60 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8185 (m-30) REVERT: B 97 GLU cc_start: 0.8434 (pt0) cc_final: 0.8226 (tp30) REVERT: B 135 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: B 146 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8134 (mtm-85) REVERT: B 291 ARG cc_start: 0.8382 (mtt180) cc_final: 0.7954 (mtm110) REVERT: B 352 ASP cc_start: 0.8750 (t0) cc_final: 0.8467 (t0) REVERT: B 423 ASP cc_start: 0.8356 (t0) cc_final: 0.8077 (t0) REVERT: B 461 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8643 (mm110) REVERT: B 550 LEU cc_start: 0.9138 (tp) cc_final: 0.8890 (mm) REVERT: B 560 LYS cc_start: 0.8867 (mttt) cc_final: 0.8392 (mmmm) REVERT: B 591 ARG cc_start: 0.8229 (ttp-170) cc_final: 0.7639 (ttm110) REVERT: A 46 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: A 66 MET cc_start: 0.8757 (mtp) cc_final: 0.8536 (mtp) REVERT: A 78 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8466 (mm-30) REVERT: A 119 GLU cc_start: 0.8448 (tt0) cc_final: 0.8137 (tt0) REVERT: A 175 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7465 (pp) REVERT: A 187 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8675 (mp) REVERT: A 275 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7448 (tptp) REVERT: A 310 ASN cc_start: 0.7741 (t0) cc_final: 0.7384 (m-40) REVERT: A 354 LYS cc_start: 0.9084 (tppt) cc_final: 0.8790 (pttt) REVERT: A 401 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8805 (ptpp) REVERT: C 60 ASP cc_start: 0.8656 (t70) cc_final: 0.7779 (t0) REVERT: C 100 MET cc_start: 0.8534 (mmm) cc_final: 0.8289 (mmp) REVERT: C 119 MET cc_start: 0.9219 (ttp) cc_final: 0.8871 (ttp) REVERT: C 226 MET cc_start: 0.8978 (mtm) cc_final: 0.8765 (mtt) REVERT: C 248 ASP cc_start: 0.8293 (m-30) cc_final: 0.8002 (m-30) REVERT: C 270 ASP cc_start: 0.8653 (m-30) cc_final: 0.8253 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7712 (t0) cc_final: 0.7180 (m-30) REVERT: C 295 ARG cc_start: 0.8849 (mmt90) cc_final: 0.8486 (mmm-85) REVERT: C 300 ASP cc_start: 0.9255 (t0) cc_final: 0.8578 (t0) REVERT: C 342 GLU cc_start: 0.8535 (tp30) cc_final: 0.8022 (tm-30) REVERT: D 20 LYS cc_start: 0.8771 (tttm) cc_final: 0.8382 (tppt) REVERT: D 104 ASP cc_start: 0.8484 (t0) cc_final: 0.8067 (t0) REVERT: D 117 ASP cc_start: 0.8236 (t0) cc_final: 0.7924 (t70) REVERT: D 175 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7679 (t0) REVERT: E 35 ASP cc_start: 0.8522 (m-30) cc_final: 0.8160 (m-30) REVERT: E 59 ASN cc_start: 0.8690 (t0) cc_final: 0.8233 (t0) REVERT: E 83 GLU cc_start: 0.8728 (pm20) cc_final: 0.8327 (pm20) REVERT: E 222 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8013 (p) REVERT: E 223 TYR cc_start: 0.8074 (m-10) cc_final: 0.7861 (m-10) REVERT: E 309 LEU cc_start: 0.8814 (mp) cc_final: 0.8038 (tt) REVERT: E 425 PHE cc_start: 0.8573 (m-80) cc_final: 0.8333 (m-80) REVERT: E 434 GLN cc_start: 0.8354 (mt0) cc_final: 0.8132 (tm-30) REVERT: E 456 ASP cc_start: 0.8702 (m-30) cc_final: 0.8439 (m-30) REVERT: E 458 LEU cc_start: 0.9260 (mt) cc_final: 0.9014 (tm) REVERT: E 468 PHE cc_start: 0.8810 (t80) cc_final: 0.8609 (t80) REVERT: E 515 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7157 (t0) REVERT: E 522 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9171 (ptmm) REVERT: E 538 PRO cc_start: 0.6875 (Cg_endo) cc_final: 0.6671 (Cg_exo) outliers start: 78 outliers final: 27 residues processed: 267 average time/residue: 1.0542 time to fit residues: 323.4659 Evaluate side-chains 218 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 91 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 VAL 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 175 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 THR 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 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 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 222 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 130 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.0980 chunk 207 optimal weight: 0.0030 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 A 203 GLN A 348 ASN C 82 GLN D 88 GLN E 266 HIS ** E 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.088903 restraints weight = 28865.302| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.56 r_work: 0.2981 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18606 Z= 0.136 Angle : 0.612 11.857 25194 Z= 0.304 Chirality : 0.042 0.173 2772 Planarity : 0.004 0.047 3187 Dihedral : 5.252 74.648 2400 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 3.34 % Allowed : 14.69 % Favored : 81.97 % 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: -0.69 (0.18), residues: 2166 helix: 0.64 (0.15), residues: 1295 sheet: -2.18 (0.70), residues: 46 loop : -2.16 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 150 HIS 0.004 0.001 HIS C 189 PHE 0.019 0.001 PHE E 468 TYR 0.027 0.001 TYR E 49 ARG 0.011 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 835) hydrogen bonds : angle 3.99110 ( 2451) metal coordination : bond 0.00465 ( 8) metal coordination : angle 6.54728 ( 12) SS BOND : bond 0.00363 ( 1) SS BOND : angle 3.55971 ( 2) covalent geometry : bond 0.00318 (18597) covalent geometry : angle 0.59416 (25180) *********************** 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 275 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8989 (mt) cc_final: 0.8489 (pp) REVERT: B 36 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7756 (mtm180) REVERT: B 43 MET cc_start: 0.7888 (mmm) cc_final: 0.7640 (mmm) REVERT: B 97 GLU cc_start: 0.8605 (pt0) cc_final: 0.8321 (tp30) REVERT: B 135 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: B 146 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8050 (mtm-85) REVERT: B 279 ASP cc_start: 0.7833 (t0) cc_final: 0.7486 (t0) REVERT: B 291 ARG cc_start: 0.8560 (mtt180) cc_final: 0.8029 (mtm110) REVERT: B 461 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8732 (mm110) REVERT: B 549 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 550 LEU cc_start: 0.9154 (tp) cc_final: 0.8921 (mm) REVERT: B 560 LYS cc_start: 0.8797 (mttt) cc_final: 0.8308 (mmmm) REVERT: B 591 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7645 (ttm110) REVERT: A 78 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8521 (mm-30) REVERT: A 119 GLU cc_start: 0.8597 (tt0) cc_final: 0.8317 (tt0) REVERT: A 175 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7259 (pp) REVERT: A 275 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7490 (tptp) REVERT: A 310 ASN cc_start: 0.7949 (t0) cc_final: 0.7588 (m-40) REVERT: A 354 LYS cc_start: 0.9110 (tppt) cc_final: 0.8789 (pttp) REVERT: A 401 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8835 (ptpp) REVERT: C 60 ASP cc_start: 0.8770 (t70) cc_final: 0.7860 (t0) REVERT: C 100 MET cc_start: 0.8631 (mmm) cc_final: 0.8409 (mmp) REVERT: C 119 MET cc_start: 0.9338 (ttp) cc_final: 0.8981 (ttp) REVERT: C 226 MET cc_start: 0.9069 (mtm) cc_final: 0.8858 (mtt) REVERT: C 248 ASP cc_start: 0.8540 (m-30) cc_final: 0.8253 (m-30) REVERT: C 270 ASP cc_start: 0.8816 (m-30) cc_final: 0.8329 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7790 (t0) cc_final: 0.7203 (m-30) REVERT: C 300 ASP cc_start: 0.9371 (t70) cc_final: 0.8840 (t0) REVERT: D 17 THR cc_start: 0.9350 (m) cc_final: 0.9073 (t) REVERT: D 19 ASP cc_start: 0.8666 (t0) cc_final: 0.8462 (t0) REVERT: D 20 LYS cc_start: 0.8768 (tttm) cc_final: 0.8349 (tppt) REVERT: D 75 ILE cc_start: 0.8496 (mp) cc_final: 0.8264 (mp) REVERT: D 104 ASP cc_start: 0.8540 (t0) cc_final: 0.8190 (t0) REVERT: D 117 ASP cc_start: 0.8312 (t0) cc_final: 0.7972 (t70) REVERT: E 35 ASP cc_start: 0.8679 (m-30) cc_final: 0.8330 (m-30) REVERT: E 59 ASN cc_start: 0.8680 (t0) cc_final: 0.8290 (t0) REVERT: E 83 GLU cc_start: 0.8816 (pm20) cc_final: 0.8477 (pm20) REVERT: E 219 GLN cc_start: 0.8115 (mt0) cc_final: 0.7882 (mt0) REVERT: E 309 LEU cc_start: 0.8824 (mp) cc_final: 0.8079 (tt) REVERT: E 456 ASP cc_start: 0.8769 (m-30) cc_final: 0.8517 (m-30) REVERT: E 458 LEU cc_start: 0.9277 (mt) cc_final: 0.9030 (tm) REVERT: E 468 PHE cc_start: 0.8792 (t80) cc_final: 0.8485 (t80) REVERT: E 515 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7227 (t0) REVERT: E 522 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9086 (ptmm) outliers start: 68 outliers final: 29 residues processed: 258 average time/residue: 1.1060 time to fit residues: 328.8617 Evaluate side-chains 219 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 146 ARG 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 151 VAL Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 175 LEU 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 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 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 E residue 222 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 38 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 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 542 GLN A 27 ASN C 82 GLN C 235 GLN D 101 ASN E 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.087371 restraints weight = 28976.514| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.73 r_work: 0.2931 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18606 Z= 0.198 Angle : 0.648 11.531 25194 Z= 0.323 Chirality : 0.044 0.289 2772 Planarity : 0.004 0.049 3187 Dihedral : 5.272 73.840 2400 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 3.29 % Allowed : 15.68 % Favored : 81.03 % 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: -0.58 (0.18), residues: 2166 helix: 0.68 (0.15), residues: 1292 sheet: -2.02 (0.73), residues: 46 loop : -2.03 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 150 HIS 0.017 0.001 HIS E 266 PHE 0.021 0.002 PHE B 2 TYR 0.025 0.002 TYR E 49 ARG 0.011 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 835) hydrogen bonds : angle 4.03227 ( 2451) metal coordination : bond 0.00337 ( 8) metal coordination : angle 6.26733 ( 12) SS BOND : bond 0.00462 ( 1) SS BOND : angle 2.40852 ( 2) covalent geometry : bond 0.00473 (18597) covalent geometry : angle 0.63365 (25180) *********************** 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 264 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 197 time to evaluate : 2.133 Fit side-chains revert: symmetry clash REVERT: B 36 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7802 (mtm180) REVERT: B 43 MET cc_start: 0.7936 (mmm) cc_final: 0.7717 (mmm) REVERT: B 97 GLU cc_start: 0.8572 (pt0) cc_final: 0.8359 (tp30) REVERT: B 135 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: B 146 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8153 (mtm-85) REVERT: B 279 ASP cc_start: 0.7904 (t0) cc_final: 0.7541 (t0) REVERT: B 291 ARG cc_start: 0.8628 (mtt180) cc_final: 0.8070 (mtm110) REVERT: B 352 ASP cc_start: 0.8764 (t0) cc_final: 0.8498 (t0) REVERT: B 461 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8782 (mm110) REVERT: B 550 LEU cc_start: 0.9184 (tp) cc_final: 0.8949 (mm) REVERT: B 560 LYS cc_start: 0.8795 (mttt) cc_final: 0.8350 (mmmt) REVERT: B 591 ARG cc_start: 0.8269 (ttp-170) cc_final: 0.7664 (ttm110) REVERT: A 76 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8863 (pt) REVERT: A 78 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8473 (mm-30) REVERT: A 119 GLU cc_start: 0.8583 (tt0) cc_final: 0.8299 (tt0) REVERT: A 175 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7465 (pp) REVERT: A 275 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7556 (tptm) REVERT: A 310 ASN cc_start: 0.8203 (t0) cc_final: 0.7901 (m-40) REVERT: A 354 LYS cc_start: 0.9134 (tppt) cc_final: 0.8811 (pttp) REVERT: A 396 ASP cc_start: 0.7193 (p0) cc_final: 0.6884 (p0) REVERT: A 401 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8874 (ptpp) REVERT: A 412 GLU cc_start: 0.7996 (tt0) cc_final: 0.7782 (tt0) REVERT: C 60 ASP cc_start: 0.8828 (t70) cc_final: 0.7927 (t0) REVERT: C 100 MET cc_start: 0.8641 (mmm) cc_final: 0.8415 (mmp) REVERT: C 119 MET cc_start: 0.9343 (ttp) cc_final: 0.8997 (ttp) REVERT: C 226 MET cc_start: 0.9072 (mtm) cc_final: 0.8863 (mtt) REVERT: C 248 ASP cc_start: 0.8594 (m-30) cc_final: 0.8313 (m-30) REVERT: C 270 ASP cc_start: 0.8830 (m-30) cc_final: 0.8321 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7813 (t0) cc_final: 0.7245 (m-30) REVERT: C 300 ASP cc_start: 0.9455 (t70) cc_final: 0.9206 (t0) REVERT: D 19 ASP cc_start: 0.8678 (t0) cc_final: 0.8446 (t0) REVERT: D 20 LYS cc_start: 0.8787 (tttm) cc_final: 0.8362 (tppt) REVERT: D 104 ASP cc_start: 0.8584 (t0) cc_final: 0.8234 (t0) REVERT: D 117 ASP cc_start: 0.8299 (t0) cc_final: 0.7943 (t70) REVERT: E 35 ASP cc_start: 0.8666 (m-30) cc_final: 0.8294 (m-30) REVERT: E 59 ASN cc_start: 0.8658 (t0) cc_final: 0.8209 (t0) REVERT: E 83 GLU cc_start: 0.8808 (pm20) cc_final: 0.8383 (pm20) REVERT: E 309 LEU cc_start: 0.8842 (mp) cc_final: 0.8123 (tt) REVERT: E 354 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7917 (tmtt) REVERT: E 425 PHE cc_start: 0.8830 (m-80) cc_final: 0.8562 (m-10) REVERT: E 456 ASP cc_start: 0.8737 (m-30) cc_final: 0.8462 (m-30) REVERT: E 458 LEU cc_start: 0.9275 (mt) cc_final: 0.9036 (tm) REVERT: E 468 PHE cc_start: 0.8757 (t80) cc_final: 0.8518 (t80) REVERT: E 515 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7304 (t0) REVERT: E 522 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9057 (ptmm) outliers start: 67 outliers final: 28 residues processed: 247 average time/residue: 1.0687 time to fit residues: 303.6267 Evaluate side-chains 221 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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 146 ARG Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 76 ILE 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 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 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 158 TYR Chi-restraints excluded: chain C residue 459 VAL 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 147 LEU Chi-restraints excluded: chain D residue 162 SER 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 515 ASP Chi-restraints excluded: chain E residue 522 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 153 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN B 474 GLN A 27 ASN C 82 GLN C 235 GLN C 303 GLN D 101 ASN E 86 HIS E 266 HIS ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.089798 restraints weight = 28705.728| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.50 r_work: 0.2971 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18606 Z= 0.138 Angle : 0.629 14.034 25194 Z= 0.308 Chirality : 0.043 0.306 2772 Planarity : 0.004 0.054 3187 Dihedral : 5.193 74.308 2400 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.00 % Favored : 93.95 % Rotamer: Outliers : 3.24 % Allowed : 16.17 % Favored : 80.59 % 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: -0.38 (0.18), residues: 2166 helix: 0.84 (0.15), residues: 1301 sheet: -1.82 (0.76), residues: 46 loop : -1.96 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 150 HIS 0.004 0.001 HIS C 189 PHE 0.019 0.001 PHE E 468 TYR 0.026 0.001 TYR E 49 ARG 0.013 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 835) hydrogen bonds : angle 3.93566 ( 2451) metal coordination : bond 0.00422 ( 8) metal coordination : angle 6.08050 ( 12) SS BOND : bond 0.00318 ( 1) SS BOND : angle 1.85235 ( 2) covalent geometry : bond 0.00323 (18597) covalent geometry : angle 0.61429 (25180) *********************** 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 274 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7798 (mtm180) REVERT: B 97 GLU cc_start: 0.8552 (pt0) cc_final: 0.8349 (tp30) REVERT: B 103 MET cc_start: 0.9286 (mtm) cc_final: 0.9064 (mtt) REVERT: B 135 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: B 139 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.7568 (mpt-90) REVERT: B 146 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8099 (mtm-85) REVERT: B 278 ASP cc_start: 0.8698 (m-30) cc_final: 0.8369 (m-30) REVERT: B 279 ASP cc_start: 0.7868 (t0) cc_final: 0.7466 (t0) REVERT: B 291 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8035 (mtm110) REVERT: B 352 ASP cc_start: 0.8724 (t0) cc_final: 0.8444 (t0) REVERT: B 542 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8705 (mt0) REVERT: B 550 LEU cc_start: 0.9170 (tp) cc_final: 0.8951 (mm) REVERT: B 560 LYS cc_start: 0.8791 (mttt) cc_final: 0.8356 (mmmt) REVERT: B 591 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7665 (ttm110) REVERT: A 76 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8889 (pt) REVERT: A 78 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8490 (mm-30) REVERT: A 119 GLU cc_start: 0.8554 (tt0) cc_final: 0.8303 (tt0) REVERT: A 175 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 275 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7508 (tptp) REVERT: A 302 SER cc_start: 0.8432 (t) cc_final: 0.8221 (t) REVERT: A 310 ASN cc_start: 0.8147 (t0) cc_final: 0.7819 (m-40) REVERT: A 354 LYS cc_start: 0.9071 (tppt) cc_final: 0.8774 (pttp) REVERT: A 396 ASP cc_start: 0.7114 (p0) cc_final: 0.6368 (p0) REVERT: A 401 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8840 (ptpp) REVERT: C 60 ASP cc_start: 0.8782 (t70) cc_final: 0.7872 (t0) REVERT: C 100 MET cc_start: 0.8632 (mmm) cc_final: 0.8396 (mmp) REVERT: C 119 MET cc_start: 0.9334 (ttp) cc_final: 0.8994 (ttp) REVERT: C 248 ASP cc_start: 0.8547 (m-30) cc_final: 0.8272 (m-30) REVERT: C 270 ASP cc_start: 0.8800 (m-30) cc_final: 0.8313 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7890 (t0) cc_final: 0.7281 (m-30) REVERT: C 300 ASP cc_start: 0.9315 (t70) cc_final: 0.9087 (t0) REVERT: C 377 LEU cc_start: 0.9341 (mt) cc_final: 0.9140 (tt) REVERT: C 406 GLN cc_start: 0.8975 (mm110) cc_final: 0.8644 (mt0) REVERT: D 17 THR cc_start: 0.9329 (m) cc_final: 0.9003 (t) REVERT: D 19 ASP cc_start: 0.8659 (t0) cc_final: 0.8415 (t0) REVERT: D 20 LYS cc_start: 0.8776 (tttm) cc_final: 0.8381 (tppt) REVERT: D 104 ASP cc_start: 0.8506 (t0) cc_final: 0.8216 (t0) REVERT: D 117 ASP cc_start: 0.8267 (t0) cc_final: 0.7915 (t70) REVERT: E 35 ASP cc_start: 0.8655 (m-30) cc_final: 0.8319 (m-30) REVERT: E 59 ASN cc_start: 0.8807 (t0) cc_final: 0.8319 (t0) REVERT: E 83 GLU cc_start: 0.8781 (pm20) cc_final: 0.8357 (pm20) REVERT: E 309 LEU cc_start: 0.8816 (mp) cc_final: 0.8132 (tt) REVERT: E 354 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7930 (tmtt) REVERT: E 425 PHE cc_start: 0.8727 (m-80) cc_final: 0.8409 (m-80) REVERT: E 456 ASP cc_start: 0.8741 (m-30) cc_final: 0.8451 (m-30) REVERT: E 458 LEU cc_start: 0.9261 (mt) cc_final: 0.9015 (tm) REVERT: E 515 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7157 (t0) REVERT: E 522 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9038 (ptmm) outliers start: 66 outliers final: 29 residues processed: 258 average time/residue: 1.0942 time to fit residues: 323.0060 Evaluate side-chains 231 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 2.055 ------------------------------------------------------------------------------- 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 139 ARG Chi-restraints excluded: chain B residue 146 ARG 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 76 ILE 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 179 LEU Chi-restraints excluded: chain A residue 195 THR 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 367 LEU 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 147 LEU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 266 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 3 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 chunk 215 optimal weight: 0.2980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 82 GLN C 235 GLN D 88 GLN E 266 HIS ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090873 restraints weight = 28574.681| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.81 r_work: 0.2977 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18606 Z= 0.126 Angle : 0.627 14.126 25194 Z= 0.304 Chirality : 0.042 0.266 2772 Planarity : 0.004 0.046 3187 Dihedral : 5.101 74.596 2400 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.00 % Favored : 93.95 % Rotamer: Outliers : 2.85 % Allowed : 17.25 % Favored : 79.90 % 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: -0.22 (0.18), residues: 2166 helix: 0.99 (0.15), residues: 1290 sheet: -1.78 (0.76), residues: 46 loop : -1.91 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 150 HIS 0.004 0.001 HIS C 189 PHE 0.015 0.001 PHE E 468 TYR 0.025 0.001 TYR E 49 ARG 0.008 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 835) hydrogen bonds : angle 3.91156 ( 2451) metal coordination : bond 0.00335 ( 8) metal coordination : angle 5.99753 ( 12) SS BOND : bond 0.00098 ( 1) SS BOND : angle 1.63969 ( 2) covalent geometry : bond 0.00291 (18597) covalent geometry : angle 0.61341 (25180) *********************** 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 271 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7899 (mt0) REVERT: B 36 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7698 (mtm180) REVERT: B 95 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7395 (t0) REVERT: B 135 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: B 146 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8225 (mtm-85) REVERT: B 278 ASP cc_start: 0.8572 (m-30) cc_final: 0.8297 (m-30) REVERT: B 279 ASP cc_start: 0.7767 (t0) cc_final: 0.7426 (t0) REVERT: B 291 ARG cc_start: 0.8402 (mtt180) cc_final: 0.7923 (mtm110) REVERT: B 352 ASP cc_start: 0.8524 (t0) cc_final: 0.8290 (t0) REVERT: B 542 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8715 (mt0) REVERT: B 549 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 550 LEU cc_start: 0.9105 (tp) cc_final: 0.8880 (mm) REVERT: B 560 LYS cc_start: 0.8828 (mttt) cc_final: 0.8432 (mmmt) REVERT: A 66 MET cc_start: 0.8899 (mtp) cc_final: 0.8344 (ttm) REVERT: A 76 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8847 (pt) REVERT: A 78 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 175 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7077 (pp) REVERT: A 275 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7489 (tptp) REVERT: A 302 SER cc_start: 0.8323 (t) cc_final: 0.8098 (t) REVERT: A 310 ASN cc_start: 0.7968 (t0) cc_final: 0.7646 (m-40) REVERT: A 333 ASN cc_start: 0.8872 (t0) cc_final: 0.7859 (t0) REVERT: C 60 ASP cc_start: 0.8547 (t70) cc_final: 0.7724 (t0) REVERT: C 100 MET cc_start: 0.8459 (mmm) cc_final: 0.8250 (mmp) REVERT: C 119 MET cc_start: 0.9163 (ttp) cc_final: 0.8828 (ttp) REVERT: C 248 ASP cc_start: 0.8281 (m-30) cc_final: 0.7983 (m-30) REVERT: C 270 ASP cc_start: 0.8654 (m-30) cc_final: 0.8237 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7828 (t0) cc_final: 0.7337 (m-30) REVERT: C 300 ASP cc_start: 0.9139 (t70) cc_final: 0.8897 (t0) REVERT: D 17 THR cc_start: 0.9248 (m) cc_final: 0.8919 (t) REVERT: D 19 ASP cc_start: 0.8594 (t0) cc_final: 0.8347 (t0) REVERT: D 20 LYS cc_start: 0.8720 (tttm) cc_final: 0.8340 (tppt) REVERT: D 89 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8769 (mmmt) REVERT: D 104 ASP cc_start: 0.8293 (t0) cc_final: 0.8053 (t0) REVERT: D 117 ASP cc_start: 0.8166 (t0) cc_final: 0.7868 (t70) REVERT: E 35 ASP cc_start: 0.8522 (m-30) cc_final: 0.8180 (m-30) REVERT: E 59 ASN cc_start: 0.8645 (t0) cc_final: 0.8286 (t0) REVERT: E 83 GLU cc_start: 0.8661 (pm20) cc_final: 0.8201 (pm20) REVERT: E 309 LEU cc_start: 0.8768 (mp) cc_final: 0.8180 (tt) REVERT: E 354 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8232 (tptm) REVERT: E 425 PHE cc_start: 0.8684 (m-80) cc_final: 0.8357 (m-80) REVERT: E 456 ASP cc_start: 0.8699 (m-30) cc_final: 0.8394 (m-30) REVERT: E 458 LEU cc_start: 0.9239 (mt) cc_final: 0.9001 (tm) REVERT: E 515 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7231 (t0) REVERT: E 522 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9026 (ptmm) outliers start: 58 outliers final: 28 residues processed: 256 average time/residue: 1.0905 time to fit residues: 320.0454 Evaluate side-chains 225 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 ARG 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 76 ILE 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 195 THR 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 367 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 354 LYS 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 150 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 208 optimal weight: 30.0000 chunk 194 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 D 88 GLN E 266 HIS ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.087797 restraints weight = 28909.047| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.77 r_work: 0.2942 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18606 Z= 0.180 Angle : 0.666 16.439 25194 Z= 0.324 Chirality : 0.044 0.235 2772 Planarity : 0.004 0.060 3187 Dihedral : 5.171 73.975 2400 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 2.70 % Allowed : 17.89 % Favored : 79.41 % 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: -0.21 (0.18), residues: 2166 helix: 0.96 (0.15), residues: 1293 sheet: -1.68 (0.76), residues: 46 loop : -1.86 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 150 HIS 0.008 0.001 HIS E 266 PHE 0.022 0.002 PHE E 468 TYR 0.025 0.001 TYR E 49 ARG 0.014 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 835) hydrogen bonds : angle 3.98984 ( 2451) metal coordination : bond 0.00300 ( 8) metal coordination : angle 6.03202 ( 12) SS BOND : bond 0.00294 ( 1) SS BOND : angle 1.67146 ( 2) covalent geometry : bond 0.00432 (18597) covalent geometry : angle 0.65326 (25180) *********************** 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 246 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7938 (mt0) REVERT: B 36 ARG cc_start: 0.8044 (mtm180) cc_final: 0.7664 (mtm180) REVERT: B 60 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: B 95 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7444 (t0) REVERT: B 135 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: B 146 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8135 (mtm-85) REVERT: B 278 ASP cc_start: 0.8606 (m-30) cc_final: 0.8383 (m-30) REVERT: B 279 ASP cc_start: 0.7717 (t0) cc_final: 0.7356 (t0) REVERT: B 291 ARG cc_start: 0.8426 (mtt180) cc_final: 0.7999 (mtm110) REVERT: B 352 ASP cc_start: 0.8554 (t0) cc_final: 0.8287 (t0) REVERT: B 549 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 550 LEU cc_start: 0.9130 (tp) cc_final: 0.8898 (mm) REVERT: B 560 LYS cc_start: 0.8827 (mttt) cc_final: 0.8432 (mmmt) REVERT: A 66 MET cc_start: 0.8913 (mtp) cc_final: 0.8324 (ttm) REVERT: A 76 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8828 (pt) REVERT: A 78 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8287 (mm-30) REVERT: A 119 GLU cc_start: 0.8270 (tt0) cc_final: 0.7938 (tt0) REVERT: A 175 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7353 (pp) REVERT: A 275 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7471 (tptm) REVERT: A 302 SER cc_start: 0.8319 (t) cc_final: 0.8087 (t) REVERT: A 310 ASN cc_start: 0.8014 (t0) cc_final: 0.7738 (m-40) REVERT: C 60 ASP cc_start: 0.8631 (t70) cc_final: 0.7711 (t0) REVERT: C 100 MET cc_start: 0.8568 (mmm) cc_final: 0.8331 (mmp) REVERT: C 119 MET cc_start: 0.9163 (ttp) cc_final: 0.8815 (ttp) REVERT: C 248 ASP cc_start: 0.8345 (m-30) cc_final: 0.8043 (m-30) REVERT: C 270 ASP cc_start: 0.8658 (m-30) cc_final: 0.8210 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7832 (t0) cc_final: 0.7339 (m-30) REVERT: C 300 ASP cc_start: 0.9191 (t70) cc_final: 0.8899 (t0) REVERT: D 17 THR cc_start: 0.9315 (m) cc_final: 0.8955 (t) REVERT: D 19 ASP cc_start: 0.8598 (t0) cc_final: 0.8329 (t0) REVERT: D 20 LYS cc_start: 0.8720 (tttm) cc_final: 0.8317 (tppt) REVERT: D 104 ASP cc_start: 0.8384 (t0) cc_final: 0.8089 (t0) REVERT: D 117 ASP cc_start: 0.8181 (t0) cc_final: 0.7846 (t70) REVERT: E 35 ASP cc_start: 0.8529 (m-30) cc_final: 0.8186 (m-30) REVERT: E 59 ASN cc_start: 0.8586 (t0) cc_final: 0.8210 (t0) REVERT: E 83 GLU cc_start: 0.8705 (pm20) cc_final: 0.8223 (pm20) REVERT: E 309 LEU cc_start: 0.8805 (mp) cc_final: 0.8242 (tt) REVERT: E 354 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8203 (tptm) REVERT: E 425 PHE cc_start: 0.8725 (m-80) cc_final: 0.8401 (m-80) REVERT: E 456 ASP cc_start: 0.8623 (m-30) cc_final: 0.8277 (m-30) REVERT: E 458 LEU cc_start: 0.9263 (mt) cc_final: 0.9009 (tm) REVERT: E 515 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7326 (t0) REVERT: E 522 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8977 (ptmm) outliers start: 55 outliers final: 32 residues processed: 231 average time/residue: 1.1029 time to fit residues: 293.2231 Evaluate side-chains 226 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 2.158 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 ARG 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 A residue 76 ILE 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 179 LEU Chi-restraints excluded: chain A residue 195 THR 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 158 TYR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 147 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 175 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 GLN A 27 ASN C 82 GLN C 235 GLN E 266 HIS ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090484 restraints weight = 28860.114| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.83 r_work: 0.2974 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18606 Z= 0.135 Angle : 0.652 16.266 25194 Z= 0.316 Chirality : 0.043 0.212 2772 Planarity : 0.004 0.063 3187 Dihedral : 5.132 74.334 2400 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 2.41 % Allowed : 18.23 % Favored : 79.36 % 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: -0.06 (0.18), residues: 2166 helix: 1.10 (0.15), residues: 1293 sheet: -1.63 (0.77), residues: 46 loop : -1.82 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 150 HIS 0.004 0.001 HIS C 189 PHE 0.013 0.001 PHE B 415 TYR 0.026 0.001 TYR E 49 ARG 0.014 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 835) hydrogen bonds : angle 3.93579 ( 2451) metal coordination : bond 0.00326 ( 8) metal coordination : angle 5.85347 ( 12) SS BOND : bond 0.00271 ( 1) SS BOND : angle 1.54123 ( 2) covalent geometry : bond 0.00319 (18597) covalent geometry : angle 0.63990 (25180) ********************** 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 248 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 2.619 Fit side-chains revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7921 (mt0) REVERT: B 36 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7657 (mtm180) REVERT: B 60 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: B 95 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7422 (t0) REVERT: B 103 MET cc_start: 0.9192 (mtt) cc_final: 0.8882 (mpp) REVERT: B 135 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8017 (pm20) REVERT: B 146 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8209 (mtm-85) REVERT: B 278 ASP cc_start: 0.8542 (m-30) cc_final: 0.8265 (m-30) REVERT: B 279 ASP cc_start: 0.7719 (t0) cc_final: 0.7441 (t0) REVERT: B 291 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7911 (mtm110) REVERT: B 352 ASP cc_start: 0.8512 (t0) cc_final: 0.8258 (t0) REVERT: B 549 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7944 (mt-10) REVERT: B 550 LEU cc_start: 0.9122 (tp) cc_final: 0.8890 (mm) REVERT: B 560 LYS cc_start: 0.8842 (mttt) cc_final: 0.8466 (mmmt) REVERT: A 66 MET cc_start: 0.8914 (mtp) cc_final: 0.8344 (ttm) REVERT: A 76 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8856 (pt) REVERT: A 78 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8315 (mm-30) REVERT: A 119 GLU cc_start: 0.8236 (tt0) cc_final: 0.7940 (tt0) REVERT: A 175 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7152 (pp) REVERT: A 275 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7460 (tptp) REVERT: A 302 SER cc_start: 0.8319 (t) cc_final: 0.8101 (t) REVERT: A 307 ARG cc_start: 0.8644 (mtt-85) cc_final: 0.8324 (mtt90) REVERT: A 310 ASN cc_start: 0.8002 (t0) cc_final: 0.7720 (m-40) REVERT: A 333 ASN cc_start: 0.8819 (t0) cc_final: 0.7780 (t0) REVERT: C 60 ASP cc_start: 0.8568 (t70) cc_final: 0.7739 (t0) REVERT: C 100 MET cc_start: 0.8479 (mmm) cc_final: 0.8260 (mmp) REVERT: C 119 MET cc_start: 0.9172 (ttp) cc_final: 0.8835 (ttp) REVERT: C 248 ASP cc_start: 0.8295 (m-30) cc_final: 0.8003 (m-30) REVERT: C 270 ASP cc_start: 0.8655 (m-30) cc_final: 0.8224 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7836 (t0) cc_final: 0.7371 (m-30) REVERT: C 300 ASP cc_start: 0.9173 (t70) cc_final: 0.8879 (t0) REVERT: D 17 THR cc_start: 0.9262 (m) cc_final: 0.8925 (t) REVERT: D 19 ASP cc_start: 0.8607 (t0) cc_final: 0.8351 (t0) REVERT: D 20 LYS cc_start: 0.8706 (tttm) cc_final: 0.8302 (tppt) REVERT: D 104 ASP cc_start: 0.8295 (t0) cc_final: 0.8044 (t0) REVERT: D 117 ASP cc_start: 0.8154 (t0) cc_final: 0.7823 (t70) REVERT: E 35 ASP cc_start: 0.8528 (m-30) cc_final: 0.8192 (m-30) REVERT: E 59 ASN cc_start: 0.8611 (t0) cc_final: 0.8288 (t0) REVERT: E 83 GLU cc_start: 0.8707 (pm20) cc_final: 0.8237 (pm20) REVERT: E 309 LEU cc_start: 0.8805 (mp) cc_final: 0.8259 (tt) REVERT: E 354 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8146 (tptm) REVERT: E 425 PHE cc_start: 0.8694 (m-80) cc_final: 0.8361 (m-80) REVERT: E 456 ASP cc_start: 0.8610 (m-30) cc_final: 0.8273 (m-30) REVERT: E 458 LEU cc_start: 0.9245 (mt) cc_final: 0.9002 (tm) REVERT: E 515 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7364 (t0) REVERT: E 522 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8945 (ptmm) outliers start: 49 outliers final: 28 residues processed: 234 average time/residue: 1.0768 time to fit residues: 289.7696 Evaluate side-chains 225 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 2.074 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 ARG 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 A residue 76 ILE 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 277 THR 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 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 367 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 354 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 186 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 203 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN C 235 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089973 restraints weight = 28807.993| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.84 r_work: 0.2993 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18606 Z= 0.122 Angle : 0.651 17.292 25194 Z= 0.314 Chirality : 0.043 0.285 2772 Planarity : 0.004 0.063 3187 Dihedral : 5.093 74.683 2400 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.04 % Rotamer: Outliers : 2.01 % Allowed : 19.12 % Favored : 78.87 % 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: 0.07 (0.18), residues: 2166 helix: 1.21 (0.15), residues: 1290 sheet: -1.51 (0.79), residues: 46 loop : -1.76 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 150 HIS 0.008 0.001 HIS E 256 PHE 0.027 0.001 PHE E 468 TYR 0.026 0.001 TYR E 49 ARG 0.014 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 835) hydrogen bonds : angle 3.88358 ( 2451) metal coordination : bond 0.00363 ( 8) metal coordination : angle 5.86450 ( 12) SS BOND : bond 0.00274 ( 1) SS BOND : angle 1.27933 ( 2) covalent geometry : bond 0.00282 (18597) covalent geometry : angle 0.63854 (25180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13464.28 seconds wall clock time: 230 minutes 7.48 seconds (13807.48 seconds total)