Starting phenix.real_space_refine on Sun Mar 17 15:09:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/03_2024/6gyu_0097.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/03_2024/6gyu_0097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/03_2024/6gyu_0097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/03_2024/6gyu_0097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/03_2024/6gyu_0097.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyu_0097/03_2024/6gyu_0097.pdb" } 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 Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.64, 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 - 3.50 Amino acid : False - 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: 7.50 Conformation dependent library (CDL) restraints added in 3.6 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: 1.67 Creating SS restraints... Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.244A pdb=" N LYS B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.526A pdb=" N PHE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.903A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 106 removed outlier: 4.171A pdb=" N MET B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 106 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.737A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.648A pdb=" N GLU B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.664A pdb=" N TRP B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.532A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 204 through 224 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.858A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 251 through 266 Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.668A pdb=" N ILE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.537A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.986A pdb=" N LEU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 394 through 422 removed outlier: 3.527A pdb=" N PHE B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 444 through 447 removed outlier: 3.871A pdb=" N HIS B 447 " --> pdb=" O ASN B 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.744A pdb=" N ASN B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.869A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 501 through 522 Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.887A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 589 through 601 removed outlier: 3.978A pdb=" N ILE B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.621A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 606 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 607' Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.673A pdb=" N PHE A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.501A pdb=" N HIS A 23 " --> pdb=" O GLU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.543A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.509A pdb=" N GLU A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.900A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.557A pdb=" N VAL A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 257 through 266 removed outlier: 3.753A pdb=" N SER A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.771A pdb=" N ILE A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.883A pdb=" N ILE A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.830A pdb=" N ASN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.797A pdb=" N VAL A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'C' and resid 56 through 72 removed outlier: 4.022A pdb=" N ASP C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 removed outlier: 3.902A pdb=" N LEU C 106 " --> pdb=" O TRP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.540A pdb=" N PHE C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.802A pdb=" N TYR C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 153 through 173 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.998A pdb=" N GLU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 193 Processing helix chain 'C' and resid 204 through 224 Processing helix chain 'C' and resid 230 through 241 removed outlier: 4.090A pdb=" N VAL C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 249 through 266 Processing helix chain 'C' and resid 279 through 303 removed outlier: 3.792A pdb=" N ILE C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 341 through 356 removed outlier: 3.687A pdb=" N TYR C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 393 through 422 Processing helix chain 'C' and resid 427 through 443 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.838A pdb=" N HIS C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.601A pdb=" N HIS C 456 " --> pdb=" O PHE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 477 removed outlier: 3.566A pdb=" N GLN C 461 " --> pdb=" O PRO C 457 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 Processing helix chain 'C' and resid 501 through 524 removed outlier: 3.576A pdb=" N ASP C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 552 removed outlier: 3.693A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.587A pdb=" N GLY C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.552A pdb=" N ASP C 605 " --> pdb=" O ASN C 602 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 606 " --> pdb=" O ILE C 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 606' Processing helix chain 'D' and resid 22 through 25 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.827A pdb=" N LYS D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 127 through 141 Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 163 through 169 removed outlier: 3.672A pdb=" N THR D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 38 through 59 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 107 through 138 removed outlier: 4.012A pdb=" N VAL E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 170 removed outlier: 4.092A pdb=" N LEU E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 183 through 193 removed outlier: 3.651A pdb=" N LYS E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 223 Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.513A pdb=" N ARG E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 334 through 349 removed outlier: 3.512A pdb=" N PHE E 338 " --> pdb=" O ARG E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 377 Processing helix chain 'E' and resid 379 through 383 removed outlier: 3.658A pdb=" N HIS E 383 " --> pdb=" O GLU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 400 through 408 Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 437 through 444 Processing helix chain 'E' and resid 451 through 479 Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 482 through 486 removed outlier: 3.704A pdb=" N GLN E 486 " --> pdb=" O ASP E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 504 removed outlier: 3.617A pdb=" N GLN E 496 " --> pdb=" O ASN E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 507 No H-bonds generated for 'chain 'E' and resid 505 through 507' Processing helix chain 'E' and resid 526 through 533 Processing sheet with id=AA1, first strand: chain 'B' and resid 152 through 153 removed outlier: 4.216A pdb=" N HIS B 152 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.657A pdb=" N VAL E 73 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.938A pdb=" N VAL A 140 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 168 through 169 removed outlier: 6.084A pdb=" N ILE A 168 " --> pdb=" O GLY A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.951A pdb=" N ILE A 276 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA8, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.675A pdb=" N LYS A 411 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 452 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 478 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 454 " --> pdb=" O ILE A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AB1, first strand: chain 'D' and resid 15 through 19 removed outlier: 4.111A pdb=" N ILE D 75 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 239 through 241 removed outlier: 3.735A pdb=" N GLN E 268 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 255 " --> pdb=" O HIS E 266 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2451 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.16 Time building geometry restraints manager: 8.13 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: 96.90 - 104.69: 281 104.69 - 112.49: 9151 112.49 - 120.28: 8446 120.28 - 128.08: 7140 128.08 - 135.88: 162 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 2.520 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 2.520 ... (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 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.900 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 51.170 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 69.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18597 Z= 0.331 Angle : 0.937 14.815 25180 Z= 0.522 Chirality : 0.053 0.300 2772 Planarity : 0.007 0.059 3187 Dihedral : 10.803 75.752 6920 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.37 % Favored : 93.35 % Rotamer: Outliers : 0.74 % Allowed : 3.69 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.13), residues: 2166 helix: -2.48 (0.10), residues: 1276 sheet: -4.11 (0.51), residues: 56 loop : -3.17 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP E 87 HIS 0.011 0.002 HIS E 43 PHE 0.033 0.003 PHE A 434 TYR 0.042 0.002 TYR A 110 ARG 0.017 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 499 time to evaluate : 2.149 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: 1.3608 time to fit residues: 768.6110 Evaluate side-chains 264 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 258 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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: 0.9980 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 0.0370 chunk 126 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- 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 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 552 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 399 GLN C 543 ASN C 552 ASN D 5 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 E 453 ASN E 471 ASN E 492 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18597 Z= 0.181 Angle : 0.610 13.191 25180 Z= 0.314 Chirality : 0.041 0.199 2772 Planarity : 0.005 0.048 3187 Dihedral : 5.772 75.558 2408 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.40 % Favored : 94.51 % Rotamer: Outliers : 3.05 % Allowed : 11.55 % Favored : 85.41 % 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: -2.36 (0.16), residues: 2166 helix: -0.75 (0.13), residues: 1313 sheet: -3.54 (0.49), residues: 65 loop : -2.72 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 150 HIS 0.010 0.001 HIS A 291 PHE 0.015 0.001 PHE B 264 TYR 0.029 0.001 TYR E 49 ARG 0.007 0.001 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 293 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 THR cc_start: 0.7650 (m) cc_final: 0.7198 (t) REVERT: B 8 LEU cc_start: 0.8845 (mt) cc_final: 0.8379 (pp) REVERT: B 25 ASP cc_start: 0.6910 (t70) cc_final: 0.6487 (t0) REVERT: B 60 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: B 97 GLU cc_start: 0.8319 (pt0) cc_final: 0.8039 (tp30) REVERT: B 146 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7562 (mtp180) REVERT: B 291 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6798 (mtm110) REVERT: B 345 TYR cc_start: 0.7995 (t80) cc_final: 0.7646 (t80) REVERT: B 352 ASP cc_start: 0.7965 (t0) cc_final: 0.7752 (t0) REVERT: B 354 ASP cc_start: 0.8336 (m-30) cc_final: 0.8073 (m-30) REVERT: B 423 ASP cc_start: 0.7778 (t0) cc_final: 0.7533 (t0) REVERT: B 550 LEU cc_start: 0.8468 (tp) cc_final: 0.8211 (mm) REVERT: B 560 LYS cc_start: 0.8469 (mttt) cc_final: 0.8027 (mmmm) REVERT: B 591 ARG cc_start: 0.7393 (mtt-85) cc_final: 0.7097 (ttm110) REVERT: A 11 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8016 (mt-10) REVERT: A 36 ILE cc_start: 0.7021 (mp) cc_final: 0.6780 (mm) REVERT: A 64 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8340 (mtp85) REVERT: A 78 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 119 GLU cc_start: 0.7886 (tt0) cc_final: 0.7671 (tt0) REVERT: A 275 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6416 (tptm) REVERT: A 282 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7535 (tmtp) REVERT: A 310 ASN cc_start: 0.6726 (t0) cc_final: 0.6359 (m-40) REVERT: A 333 ASN cc_start: 0.8624 (t0) cc_final: 0.8297 (m-40) REVERT: A 336 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7051 (mmtt) REVERT: A 354 LYS cc_start: 0.8843 (tppt) cc_final: 0.8444 (pttp) REVERT: A 388 LYS cc_start: 0.8504 (tttt) cc_final: 0.8289 (mtpp) REVERT: A 393 LYS cc_start: 0.7489 (ttpt) cc_final: 0.7251 (ttmt) REVERT: A 401 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8344 (ptpp) REVERT: A 407 HIS cc_start: 0.9066 (m-70) cc_final: 0.8822 (m-70) REVERT: A 420 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8490 (tp40) REVERT: C 60 ASP cc_start: 0.8234 (t70) cc_final: 0.7261 (t0) REVERT: C 120 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8386 (mt-10) REVERT: C 150 LYS cc_start: 0.9001 (mttm) cc_final: 0.8687 (tptt) REVERT: C 185 VAL cc_start: 0.7458 (OUTLIER) cc_final: 0.7235 (t) REVERT: C 248 ASP cc_start: 0.7895 (m-30) cc_final: 0.7472 (m-30) REVERT: C 270 ASP cc_start: 0.8379 (m-30) cc_final: 0.7880 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7175 (t0) cc_final: 0.6712 (m-30) REVERT: C 342 GLU cc_start: 0.8575 (tp30) cc_final: 0.7550 (tm-30) REVERT: C 347 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8262 (mmtt) REVERT: C 368 LYS cc_start: 0.8709 (mttm) cc_final: 0.8446 (ptmm) REVERT: C 382 TYR cc_start: 0.8628 (t80) cc_final: 0.8416 (t80) REVERT: C 387 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8867 (mp) REVERT: C 433 HIS cc_start: 0.8375 (t-90) cc_final: 0.8162 (t70) REVERT: D 20 LYS cc_start: 0.8137 (tttm) cc_final: 0.7632 (tttt) REVERT: D 34 ASN cc_start: 0.7404 (m-40) cc_final: 0.6952 (m-40) REVERT: D 95 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7933 (mt-10) REVERT: D 98 ARG cc_start: 0.8769 (ttp-110) cc_final: 0.8460 (ttm110) REVERT: D 104 ASP cc_start: 0.8318 (t0) cc_final: 0.7797 (t0) REVERT: D 117 ASP cc_start: 0.7697 (t0) cc_final: 0.7182 (t70) REVERT: D 127 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: D 165 GLU cc_start: 0.8520 (pp20) cc_final: 0.8118 (pm20) REVERT: E 31 GLN cc_start: 0.7910 (mm-40) cc_final: 0.6902 (tp40) REVERT: E 35 ASP cc_start: 0.8379 (m-30) cc_final: 0.7966 (m-30) REVERT: E 59 ASN cc_start: 0.8173 (t0) cc_final: 0.7574 (t0) REVERT: E 163 ASP cc_start: 0.8731 (m-30) cc_final: 0.8502 (p0) REVERT: E 309 LEU cc_start: 0.8903 (mp) cc_final: 0.7866 (tt) REVERT: E 329 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8422 (tm) REVERT: E 336 GLU cc_start: 0.8486 (pm20) cc_final: 0.8060 (tp30) REVERT: E 434 GLN cc_start: 0.8452 (mt0) cc_final: 0.8072 (tm-30) REVERT: E 456 ASP cc_start: 0.8720 (m-30) cc_final: 0.8358 (m-30) REVERT: E 466 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8467 (mm-30) REVERT: E 468 PHE cc_start: 0.8699 (t80) cc_final: 0.8081 (t80) REVERT: E 479 PHE cc_start: 0.8585 (m-80) cc_final: 0.8137 (m-80) REVERT: E 515 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7438 (t0) outliers start: 62 outliers final: 15 residues processed: 336 average time/residue: 1.1815 time to fit residues: 448.4276 Evaluate side-chains 251 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 377 LEU 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 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 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 127 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN B 461 GLN B 474 GLN A 27 ASN A 171 ASN C 82 GLN C 235 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 444 ASN D 34 ASN E 219 GLN E 266 HIS E 445 HIS E 453 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18597 Z= 0.395 Angle : 0.668 9.855 25180 Z= 0.344 Chirality : 0.045 0.175 2772 Planarity : 0.005 0.050 3187 Dihedral : 5.615 73.553 2400 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.51 % Favored : 93.35 % Rotamer: Outliers : 3.69 % Allowed : 13.46 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.57 (0.17), residues: 2166 helix: -0.12 (0.14), residues: 1313 sheet: -2.61 (0.65), residues: 46 loop : -2.46 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 150 HIS 0.019 0.002 HIS E 266 PHE 0.026 0.002 PHE B 2 TYR 0.029 0.002 TYR E 49 ARG 0.008 0.001 ARG B 19 *********************** 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 fitting. rotamer outliers: 75 poor density : 220 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7960 (tp40) REVERT: B 8 LEU cc_start: 0.8904 (mt) cc_final: 0.8385 (pp) REVERT: B 25 ASP cc_start: 0.6631 (t70) cc_final: 0.6406 (OUTLIER) REVERT: B 43 MET cc_start: 0.7717 (mmm) cc_final: 0.7429 (mmm) REVERT: B 135 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: B 141 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8342 (mm-30) REVERT: B 221 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7982 (mttm) REVERT: B 291 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6747 (mtm110) REVERT: B 345 TYR cc_start: 0.8002 (t80) cc_final: 0.7801 (t80) REVERT: B 423 ASP cc_start: 0.7807 (t0) cc_final: 0.7573 (t0) REVERT: B 560 LYS cc_start: 0.8437 (mttt) cc_final: 0.8023 (mmmm) REVERT: A 11 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8186 (mt-10) REVERT: A 46 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8390 (mm-30) REVERT: A 64 ARG cc_start: 0.8659 (ttt180) cc_final: 0.8296 (ttp80) REVERT: A 78 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7796 (mm-30) REVERT: A 119 GLU cc_start: 0.7991 (tt0) cc_final: 0.7376 (tt0) REVERT: A 175 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7331 (pp) REVERT: A 183 CYS cc_start: 0.8293 (t) cc_final: 0.7974 (m) REVERT: A 275 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6313 (tptp) REVERT: A 282 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7854 (tttm) REVERT: A 310 ASN cc_start: 0.7213 (t0) cc_final: 0.6823 (m-40) REVERT: A 354 LYS cc_start: 0.9015 (tppt) cc_final: 0.8532 (pttt) REVERT: A 388 LYS cc_start: 0.8660 (tttt) cc_final: 0.8398 (mtpp) REVERT: A 401 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8397 (ptpp) REVERT: C 60 ASP cc_start: 0.8297 (t70) cc_final: 0.7321 (t0) REVERT: C 100 MET cc_start: 0.8190 (mmm) cc_final: 0.7813 (mmp) REVERT: C 119 MET cc_start: 0.8728 (ttp) cc_final: 0.8276 (ttp) REVERT: C 150 LYS cc_start: 0.9040 (mttm) cc_final: 0.8733 (tptt) REVERT: C 185 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7307 (t) REVERT: C 226 MET cc_start: 0.8583 (mtm) cc_final: 0.8240 (mtt) REVERT: C 248 ASP cc_start: 0.7956 (m-30) cc_final: 0.7565 (m-30) REVERT: C 270 ASP cc_start: 0.8386 (m-30) cc_final: 0.7877 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7253 (t0) cc_final: 0.6736 (m-30) REVERT: C 342 GLU cc_start: 0.8603 (tp30) cc_final: 0.7621 (tm-30) REVERT: C 368 LYS cc_start: 0.8837 (mttm) cc_final: 0.8589 (ptmm) REVERT: C 382 TYR cc_start: 0.8683 (t80) cc_final: 0.8477 (t80) REVERT: C 387 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8841 (mp) REVERT: D 17 THR cc_start: 0.9235 (m) cc_final: 0.9025 (t) REVERT: D 20 LYS cc_start: 0.8161 (tttm) cc_final: 0.7786 (tppt) REVERT: D 34 ASN cc_start: 0.7350 (m110) cc_final: 0.7100 (m-40) REVERT: D 104 ASP cc_start: 0.8498 (t0) cc_final: 0.7993 (t0) REVERT: D 117 ASP cc_start: 0.7618 (t0) cc_final: 0.7139 (t70) REVERT: D 165 GLU cc_start: 0.8639 (pp20) cc_final: 0.8401 (pt0) REVERT: E 35 ASP cc_start: 0.8365 (m-30) cc_final: 0.7951 (m-30) REVERT: E 59 ASN cc_start: 0.7985 (t0) cc_final: 0.7316 (t0) REVERT: E 163 ASP cc_start: 0.8771 (m-30) cc_final: 0.8512 (p0) REVERT: E 309 LEU cc_start: 0.8935 (mp) cc_final: 0.7961 (tt) REVERT: E 425 PHE cc_start: 0.8729 (m-80) cc_final: 0.8466 (m-10) REVERT: E 434 GLN cc_start: 0.8507 (mt0) cc_final: 0.8202 (tm-30) REVERT: E 456 ASP cc_start: 0.8594 (m-30) cc_final: 0.8361 (m-30) REVERT: E 468 PHE cc_start: 0.8759 (t80) cc_final: 0.8493 (t80) REVERT: E 479 PHE cc_start: 0.8613 (m-80) cc_final: 0.8071 (m-10) REVERT: E 522 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9152 (ptmm) outliers start: 75 outliers final: 33 residues processed: 272 average time/residue: 1.1224 time to fit residues: 348.6555 Evaluate side-chains 233 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 221 LYS Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 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 186 ILE 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 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 185 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 HIS Chi-restraints excluded: chain E residue 266 HIS Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 522 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 198 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 235 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN E 219 GLN E 266 HIS E 492 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18597 Z= 0.204 Angle : 0.582 9.295 25180 Z= 0.299 Chirality : 0.041 0.166 2772 Planarity : 0.004 0.050 3187 Dihedral : 5.410 74.507 2400 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.64 % Rotamer: Outliers : 3.78 % Allowed : 14.45 % Favored : 81.77 % 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: -0.93 (0.18), residues: 2166 helix: 0.46 (0.15), residues: 1292 sheet: -2.10 (0.72), residues: 46 loop : -2.30 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 150 HIS 0.011 0.001 HIS E 266 PHE 0.023 0.001 PHE E 468 TYR 0.028 0.001 TYR E 49 ARG 0.010 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 215 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8078 (tp40) REVERT: B 8 LEU cc_start: 0.8897 (mt) cc_final: 0.8357 (pp) REVERT: B 36 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7748 (mtm180) REVERT: B 135 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: B 141 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8271 (mm-30) REVERT: B 291 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6791 (mtm110) REVERT: B 345 TYR cc_start: 0.8029 (t80) cc_final: 0.7784 (t80) REVERT: B 352 ASP cc_start: 0.8029 (t0) cc_final: 0.7625 (t0) REVERT: B 423 ASP cc_start: 0.7794 (t0) cc_final: 0.7542 (t0) REVERT: B 550 LEU cc_start: 0.8579 (tp) cc_final: 0.8303 (mm) REVERT: B 560 LYS cc_start: 0.8400 (mttt) cc_final: 0.7964 (mmmm) REVERT: A 11 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8149 (mt-10) REVERT: A 64 ARG cc_start: 0.8651 (ttt180) cc_final: 0.8290 (ttp80) REVERT: A 78 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7720 (mm-30) REVERT: A 119 GLU cc_start: 0.7699 (tt0) cc_final: 0.7468 (tt0) REVERT: A 163 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 175 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7103 (pp) REVERT: A 275 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6287 (tptp) REVERT: A 282 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7834 (tttm) REVERT: A 310 ASN cc_start: 0.7119 (t0) cc_final: 0.6690 (m-40) REVERT: A 354 LYS cc_start: 0.8935 (tppt) cc_final: 0.8488 (pttt) REVERT: A 388 LYS cc_start: 0.8636 (tttt) cc_final: 0.8214 (mtmt) REVERT: A 401 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8417 (ptpp) REVERT: C 60 ASP cc_start: 0.8167 (t70) cc_final: 0.7132 (t0) REVERT: C 100 MET cc_start: 0.8141 (mmm) cc_final: 0.7939 (mmp) REVERT: C 119 MET cc_start: 0.8775 (ttp) cc_final: 0.8317 (ttp) REVERT: C 150 LYS cc_start: 0.9030 (mttm) cc_final: 0.8736 (tptt) REVERT: C 226 MET cc_start: 0.8496 (mtm) cc_final: 0.8121 (mtt) REVERT: C 248 ASP cc_start: 0.7885 (m-30) cc_final: 0.7415 (m-30) REVERT: C 270 ASP cc_start: 0.8386 (m-30) cc_final: 0.7886 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7212 (t0) cc_final: 0.6713 (m-30) REVERT: C 368 LYS cc_start: 0.8823 (mttm) cc_final: 0.8578 (ptmm) REVERT: C 591 ARG cc_start: 0.5911 (mpt180) cc_final: 0.5671 (mpp-170) REVERT: D 20 LYS cc_start: 0.8090 (tttm) cc_final: 0.7704 (tppt) REVERT: D 104 ASP cc_start: 0.8398 (t0) cc_final: 0.7927 (t0) REVERT: D 117 ASP cc_start: 0.7625 (t0) cc_final: 0.7159 (t70) REVERT: D 165 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: E 35 ASP cc_start: 0.8323 (m-30) cc_final: 0.7968 (m-30) REVERT: E 59 ASN cc_start: 0.8001 (t0) cc_final: 0.7318 (t0) REVERT: E 83 GLU cc_start: 0.8388 (pm20) cc_final: 0.7871 (pm20) REVERT: E 163 ASP cc_start: 0.8720 (m-30) cc_final: 0.8484 (p0) REVERT: E 247 ASP cc_start: 0.8374 (m-30) cc_final: 0.8108 (t0) REVERT: E 279 PHE cc_start: 0.8052 (m-80) cc_final: 0.7708 (m-80) REVERT: E 309 LEU cc_start: 0.8891 (mp) cc_final: 0.8107 (tt) REVERT: E 336 GLU cc_start: 0.8803 (mp0) cc_final: 0.8336 (pm20) REVERT: E 407 MET cc_start: 0.8013 (mmm) cc_final: 0.7512 (mtp) REVERT: E 425 PHE cc_start: 0.8793 (m-80) cc_final: 0.8515 (m-10) REVERT: E 434 GLN cc_start: 0.8441 (mt0) cc_final: 0.8232 (tm-30) REVERT: E 455 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7743 (pmm-80) REVERT: E 456 ASP cc_start: 0.8707 (m-30) cc_final: 0.8385 (m-30) REVERT: E 458 LEU cc_start: 0.9259 (mt) cc_final: 0.8979 (tm) REVERT: E 468 PHE cc_start: 0.8796 (t80) cc_final: 0.8510 (t80) REVERT: E 478 PHE cc_start: 0.8310 (m-10) cc_final: 0.7490 (m-80) REVERT: E 479 PHE cc_start: 0.8584 (m-80) cc_final: 0.7998 (m-10) REVERT: E 515 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7318 (t0) outliers start: 77 outliers final: 31 residues processed: 271 average time/residue: 1.0627 time to fit residues: 329.9253 Evaluate side-chains 229 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS 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 343 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 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 338 VAL 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 289 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 455 ARG Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 533 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 235 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN D 88 GLN D 101 ASN E 219 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18597 Z= 0.271 Angle : 0.614 10.263 25180 Z= 0.310 Chirality : 0.043 0.316 2772 Planarity : 0.004 0.049 3187 Dihedral : 5.315 74.275 2400 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.09 % Favored : 93.81 % Rotamer: Outliers : 3.69 % Allowed : 14.74 % Favored : 81.57 % 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: 0.61 (0.15), residues: 1302 sheet: -1.97 (0.73), residues: 46 loop : -2.15 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 150 HIS 0.005 0.001 HIS B 189 PHE 0.020 0.002 PHE B 2 TYR 0.026 0.001 TYR E 49 ARG 0.011 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 215 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8110 (tp40) REVERT: B 8 LEU cc_start: 0.8930 (mt) cc_final: 0.8368 (pp) REVERT: B 36 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7673 (mtm180) REVERT: B 135 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 141 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8267 (mm-30) REVERT: B 279 ASP cc_start: 0.7014 (t0) cc_final: 0.6644 (t0) REVERT: B 291 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6799 (mtm110) REVERT: B 345 TYR cc_start: 0.8025 (t80) cc_final: 0.7807 (t80) REVERT: B 423 ASP cc_start: 0.7819 (t0) cc_final: 0.7540 (t0) REVERT: B 550 LEU cc_start: 0.8600 (tp) cc_final: 0.8329 (mm) REVERT: B 560 LYS cc_start: 0.8328 (mttt) cc_final: 0.7933 (mmmt) REVERT: A 11 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8216 (mt-10) REVERT: A 64 ARG cc_start: 0.8648 (ttt180) cc_final: 0.8302 (ttp80) REVERT: A 78 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7692 (mm-30) REVERT: A 119 GLU cc_start: 0.7667 (tt0) cc_final: 0.7377 (tt0) REVERT: A 163 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8078 (mm) REVERT: A 175 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7145 (pp) REVERT: A 275 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6328 (tptm) REVERT: A 282 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7962 (tttm) REVERT: A 310 ASN cc_start: 0.7279 (t0) cc_final: 0.6866 (m-40) REVERT: A 354 LYS cc_start: 0.8938 (tppt) cc_final: 0.8529 (pttp) REVERT: A 388 LYS cc_start: 0.8508 (tttt) cc_final: 0.8080 (mtmt) REVERT: A 401 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8543 (mtpp) REVERT: A 412 GLU cc_start: 0.6545 (tt0) cc_final: 0.6336 (tt0) REVERT: C 60 ASP cc_start: 0.8213 (t70) cc_final: 0.7188 (t0) REVERT: C 100 MET cc_start: 0.8117 (mmm) cc_final: 0.7888 (mmp) REVERT: C 119 MET cc_start: 0.8740 (ttp) cc_final: 0.8289 (ttp) REVERT: C 150 LYS cc_start: 0.9033 (mttm) cc_final: 0.8734 (tptt) REVERT: C 226 MET cc_start: 0.8504 (mtm) cc_final: 0.8140 (mtt) REVERT: C 248 ASP cc_start: 0.7897 (m-30) cc_final: 0.7424 (m-30) REVERT: C 270 ASP cc_start: 0.8390 (m-30) cc_final: 0.7887 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7369 (t0) cc_final: 0.6866 (m-30) REVERT: C 300 ASP cc_start: 0.8579 (t70) cc_final: 0.8284 (t0) REVERT: C 368 LYS cc_start: 0.8836 (mttm) cc_final: 0.8594 (ptmm) REVERT: C 591 ARG cc_start: 0.6016 (mpt180) cc_final: 0.5779 (mpp-170) REVERT: D 20 LYS cc_start: 0.8094 (tttm) cc_final: 0.7702 (tppt) REVERT: D 104 ASP cc_start: 0.8417 (t0) cc_final: 0.7940 (t0) REVERT: D 117 ASP cc_start: 0.7495 (t0) cc_final: 0.7018 (t70) REVERT: E 35 ASP cc_start: 0.8332 (m-30) cc_final: 0.7989 (m-30) REVERT: E 59 ASN cc_start: 0.7854 (t0) cc_final: 0.7189 (t0) REVERT: E 83 GLU cc_start: 0.8356 (pm20) cc_final: 0.7756 (pm20) REVERT: E 163 ASP cc_start: 0.8724 (m-30) cc_final: 0.8476 (p0) REVERT: E 247 ASP cc_start: 0.8349 (m-30) cc_final: 0.8054 (t0) REVERT: E 309 LEU cc_start: 0.8899 (mp) cc_final: 0.8147 (tt) REVERT: E 336 GLU cc_start: 0.8787 (mp0) cc_final: 0.8326 (pm20) REVERT: E 407 MET cc_start: 0.7844 (mmm) cc_final: 0.7414 (mtp) REVERT: E 455 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7748 (pmm-80) REVERT: E 456 ASP cc_start: 0.8695 (m-30) cc_final: 0.8364 (m-30) REVERT: E 458 LEU cc_start: 0.9273 (mt) cc_final: 0.9024 (tm) REVERT: E 468 PHE cc_start: 0.8803 (t80) cc_final: 0.8593 (t80) REVERT: E 478 PHE cc_start: 0.8357 (m-10) cc_final: 0.7560 (m-80) REVERT: E 479 PHE cc_start: 0.8650 (m-80) cc_final: 0.8007 (m-10) outliers start: 75 outliers final: 34 residues processed: 267 average time/residue: 1.0691 time to fit residues: 327.5122 Evaluate side-chains 235 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 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 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 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 455 ARG Chi-restraints excluded: chain E residue 515 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 GLN C 82 GLN C 235 GLN C 303 GLN D 88 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18597 Z= 0.184 Angle : 0.582 13.231 25180 Z= 0.293 Chirality : 0.042 0.301 2772 Planarity : 0.004 0.047 3187 Dihedral : 5.206 74.902 2400 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.41 % Rotamer: Outliers : 3.14 % Allowed : 15.33 % Favored : 81.52 % 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: -0.43 (0.18), residues: 2166 helix: 0.85 (0.15), residues: 1294 sheet: -1.79 (0.75), residues: 46 loop : -2.07 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 65 HIS 0.004 0.001 HIS B 189 PHE 0.019 0.001 PHE E 468 TYR 0.026 0.001 TYR E 49 ARG 0.012 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 224 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8096 (tp40) REVERT: B 8 LEU cc_start: 0.8948 (mt) cc_final: 0.8380 (pp) REVERT: B 36 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7660 (mtm180) REVERT: B 135 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: B 139 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7181 (mpt-90) REVERT: B 141 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8289 (mm-30) REVERT: B 146 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7430 (mtp180) REVERT: B 279 ASP cc_start: 0.6903 (t0) cc_final: 0.6536 (t0) REVERT: B 291 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6815 (mtm110) REVERT: B 345 TYR cc_start: 0.8051 (t80) cc_final: 0.7812 (t80) REVERT: B 542 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: B 550 LEU cc_start: 0.8583 (tp) cc_final: 0.8327 (mm) REVERT: B 560 LYS cc_start: 0.8326 (mttt) cc_final: 0.7932 (mmmt) REVERT: A 11 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8210 (mt-10) REVERT: A 64 ARG cc_start: 0.8664 (ttt180) cc_final: 0.8311 (ttp80) REVERT: A 78 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 119 GLU cc_start: 0.7735 (tt0) cc_final: 0.7492 (tt0) REVERT: A 163 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8092 (mm) REVERT: A 175 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6961 (pp) REVERT: A 275 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6329 (tptm) REVERT: A 282 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7903 (tttm) REVERT: A 302 SER cc_start: 0.7593 (t) cc_final: 0.7036 (t) REVERT: A 310 ASN cc_start: 0.7232 (t0) cc_final: 0.6794 (m-40) REVERT: A 333 ASN cc_start: 0.8754 (t0) cc_final: 0.7557 (t0) REVERT: A 354 LYS cc_start: 0.8879 (tppt) cc_final: 0.8522 (pttp) REVERT: A 400 THR cc_start: 0.9197 (m) cc_final: 0.8958 (p) REVERT: A 401 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8413 (ptpp) REVERT: C 60 ASP cc_start: 0.8183 (t70) cc_final: 0.7134 (t0) REVERT: C 100 MET cc_start: 0.8103 (mmm) cc_final: 0.7857 (mmp) REVERT: C 119 MET cc_start: 0.8754 (ttp) cc_final: 0.8316 (ttp) REVERT: C 150 LYS cc_start: 0.9021 (mttm) cc_final: 0.8732 (tptt) REVERT: C 226 MET cc_start: 0.8455 (mtm) cc_final: 0.8255 (mtp) REVERT: C 248 ASP cc_start: 0.7882 (m-30) cc_final: 0.7405 (m-30) REVERT: C 270 ASP cc_start: 0.8385 (m-30) cc_final: 0.7844 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7387 (t0) cc_final: 0.6893 (m-30) REVERT: C 300 ASP cc_start: 0.8616 (t70) cc_final: 0.7526 (t0) REVERT: C 368 LYS cc_start: 0.8846 (mttm) cc_final: 0.8600 (ptmm) REVERT: C 591 ARG cc_start: 0.5999 (mpt180) cc_final: 0.5764 (mpp-170) REVERT: D 17 THR cc_start: 0.9294 (m) cc_final: 0.9034 (t) REVERT: D 20 LYS cc_start: 0.8094 (tttm) cc_final: 0.7698 (tppt) REVERT: D 104 ASP cc_start: 0.8316 (t0) cc_final: 0.7862 (t0) REVERT: D 117 ASP cc_start: 0.7524 (t0) cc_final: 0.7031 (t70) REVERT: E 35 ASP cc_start: 0.8349 (m-30) cc_final: 0.8004 (m-30) REVERT: E 59 ASN cc_start: 0.7919 (t0) cc_final: 0.7273 (t0) REVERT: E 83 GLU cc_start: 0.8335 (pm20) cc_final: 0.8091 (pm20) REVERT: E 163 ASP cc_start: 0.8786 (m-30) cc_final: 0.8548 (p0) REVERT: E 247 ASP cc_start: 0.8308 (m-30) cc_final: 0.8015 (t0) REVERT: E 309 LEU cc_start: 0.8895 (mp) cc_final: 0.8160 (tt) REVERT: E 354 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7736 (tmtt) REVERT: E 407 MET cc_start: 0.7803 (mmm) cc_final: 0.7519 (mtp) REVERT: E 425 PHE cc_start: 0.8901 (m-80) cc_final: 0.8639 (m-80) REVERT: E 455 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7829 (pmm-80) REVERT: E 456 ASP cc_start: 0.8700 (m-30) cc_final: 0.8362 (m-30) REVERT: E 458 LEU cc_start: 0.9273 (mt) cc_final: 0.9027 (tm) REVERT: E 478 PHE cc_start: 0.8372 (m-10) cc_final: 0.7717 (m-80) REVERT: E 479 PHE cc_start: 0.8649 (m-80) cc_final: 0.7993 (m-10) outliers start: 64 outliers final: 35 residues processed: 271 average time/residue: 1.0368 time to fit residues: 322.8899 Evaluate side-chains 239 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 39 ASP 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 226 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 542 GLN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 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 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 455 ARG Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 515 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 235 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18597 Z= 0.289 Angle : 0.626 13.028 25180 Z= 0.314 Chirality : 0.044 0.245 2772 Planarity : 0.004 0.054 3187 Dihedral : 5.218 74.206 2400 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.00 % Favored : 93.91 % Rotamer: Outliers : 3.29 % Allowed : 16.07 % Favored : 80.64 % 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: -0.42 (0.18), residues: 2166 helix: 0.83 (0.15), residues: 1303 sheet: -1.73 (0.75), residues: 46 loop : -2.05 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 65 HIS 0.005 0.001 HIS C 433 PHE 0.019 0.002 PHE B 2 TYR 0.025 0.001 TYR E 49 ARG 0.011 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 202 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7661 (mtm180) REVERT: B 60 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: B 135 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 279 ASP cc_start: 0.7005 (t0) cc_final: 0.6647 (t0) REVERT: B 291 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6798 (mtm110) REVERT: B 345 TYR cc_start: 0.8034 (t80) cc_final: 0.7785 (t80) REVERT: B 550 LEU cc_start: 0.8594 (tp) cc_final: 0.8329 (mm) REVERT: B 560 LYS cc_start: 0.8378 (mttt) cc_final: 0.7998 (mmmt) REVERT: B 591 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6916 (ttm110) REVERT: A 11 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8285 (mt-10) REVERT: A 64 ARG cc_start: 0.8678 (ttt180) cc_final: 0.8320 (ttp80) REVERT: A 78 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 163 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7976 (mm) REVERT: A 175 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7067 (pp) REVERT: A 275 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6329 (tptm) REVERT: A 282 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7925 (tttm) REVERT: A 302 SER cc_start: 0.7865 (t) cc_final: 0.7571 (t) REVERT: A 310 ASN cc_start: 0.7265 (t0) cc_final: 0.6874 (m-40) REVERT: A 354 LYS cc_start: 0.8889 (tppt) cc_final: 0.8523 (pttp) REVERT: A 394 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 401 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8588 (mtpp) REVERT: A 412 GLU cc_start: 0.6640 (tt0) cc_final: 0.6373 (tt0) REVERT: A 413 LEU cc_start: 0.7459 (mt) cc_final: 0.7254 (mt) REVERT: C 60 ASP cc_start: 0.8215 (t70) cc_final: 0.7167 (t0) REVERT: C 100 MET cc_start: 0.8126 (mmm) cc_final: 0.7869 (mmp) REVERT: C 119 MET cc_start: 0.8748 (ttp) cc_final: 0.8317 (ttp) REVERT: C 150 LYS cc_start: 0.9039 (mttm) cc_final: 0.8749 (tptt) REVERT: C 248 ASP cc_start: 0.7926 (m-30) cc_final: 0.7475 (m-30) REVERT: C 270 ASP cc_start: 0.8400 (m-30) cc_final: 0.7839 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7408 (t0) cc_final: 0.6940 (m-30) REVERT: C 300 ASP cc_start: 0.8684 (t70) cc_final: 0.7447 (t0) REVERT: C 368 LYS cc_start: 0.8844 (mttm) cc_final: 0.8592 (ptmm) REVERT: C 591 ARG cc_start: 0.5943 (mpt180) cc_final: 0.5716 (mpp-170) REVERT: D 20 LYS cc_start: 0.8116 (tttm) cc_final: 0.7702 (tppt) REVERT: D 104 ASP cc_start: 0.8373 (t0) cc_final: 0.7897 (t0) REVERT: D 117 ASP cc_start: 0.7479 (t0) cc_final: 0.6964 (t70) REVERT: E 35 ASP cc_start: 0.8333 (m-30) cc_final: 0.7984 (m-30) REVERT: E 59 ASN cc_start: 0.7931 (t0) cc_final: 0.7239 (t0) REVERT: E 83 GLU cc_start: 0.8379 (pm20) cc_final: 0.7904 (pm20) REVERT: E 163 ASP cc_start: 0.8788 (m-30) cc_final: 0.8554 (p0) REVERT: E 247 ASP cc_start: 0.8295 (m-30) cc_final: 0.7981 (t0) REVERT: E 280 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6102 (mp) REVERT: E 309 LEU cc_start: 0.8905 (mp) cc_final: 0.8204 (tt) REVERT: E 336 GLU cc_start: 0.8764 (mp0) cc_final: 0.8360 (pm20) REVERT: E 354 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7739 (tmtt) REVERT: E 407 MET cc_start: 0.7724 (mmm) cc_final: 0.7447 (mtp) REVERT: E 425 PHE cc_start: 0.8857 (m-80) cc_final: 0.8550 (m-80) REVERT: E 455 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7823 (pmm-80) REVERT: E 456 ASP cc_start: 0.8724 (m-30) cc_final: 0.8384 (m-30) REVERT: E 458 LEU cc_start: 0.9284 (mt) cc_final: 0.9038 (tm) REVERT: E 478 PHE cc_start: 0.8416 (m-10) cc_final: 0.7868 (m-80) outliers start: 67 outliers final: 36 residues processed: 250 average time/residue: 1.0804 time to fit residues: 310.4629 Evaluate side-chains 239 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 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 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 459 VAL Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 455 ARG Chi-restraints excluded: chain E residue 515 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 103 optimal weight: 0.0070 chunk 19 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 235 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18597 Z= 0.161 Angle : 0.583 15.173 25180 Z= 0.289 Chirality : 0.041 0.242 2772 Planarity : 0.004 0.053 3187 Dihedral : 5.077 75.180 2400 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 2.80 % Allowed : 16.86 % Favored : 80.34 % 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: -0.11 (0.18), residues: 2166 helix: 1.13 (0.15), residues: 1294 sheet: -1.51 (0.76), residues: 46 loop : -2.00 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 65 HIS 0.003 0.001 HIS D 96 PHE 0.019 0.001 PHE E 468 TYR 0.026 0.001 TYR E 49 ARG 0.013 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7430 (mtm180) REVERT: B 60 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: B 103 MET cc_start: 0.8585 (mtm) cc_final: 0.8315 (mtt) REVERT: B 135 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: B 146 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7397 (mtp180) REVERT: B 279 ASP cc_start: 0.6898 (t0) cc_final: 0.6524 (t0) REVERT: B 291 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6777 (mtm110) REVERT: B 345 TYR cc_start: 0.8067 (t80) cc_final: 0.7818 (t80) REVERT: B 550 LEU cc_start: 0.8553 (tp) cc_final: 0.8310 (mm) REVERT: B 560 LYS cc_start: 0.8350 (mttt) cc_final: 0.7991 (mmmt) REVERT: B 591 ARG cc_start: 0.7344 (mtt-85) cc_final: 0.6877 (ttm110) REVERT: A 11 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8179 (mt-10) REVERT: A 64 ARG cc_start: 0.8670 (ttt180) cc_final: 0.8400 (mtp85) REVERT: A 78 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 119 GLU cc_start: 0.7753 (tt0) cc_final: 0.7290 (tt0) REVERT: A 163 LEU cc_start: 0.8270 (mm) cc_final: 0.7938 (mm) REVERT: A 175 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6703 (pp) REVERT: A 275 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6329 (tptm) REVERT: A 282 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7863 (tttm) REVERT: A 302 SER cc_start: 0.7877 (t) cc_final: 0.7590 (t) REVERT: A 310 ASN cc_start: 0.7183 (t0) cc_final: 0.6785 (m-40) REVERT: A 333 ASN cc_start: 0.8698 (t0) cc_final: 0.8432 (m-40) REVERT: A 354 LYS cc_start: 0.8768 (tppt) cc_final: 0.8430 (pttp) REVERT: A 355 ASN cc_start: 0.8470 (t0) cc_final: 0.8135 (m-40) REVERT: A 400 THR cc_start: 0.9152 (m) cc_final: 0.8918 (p) REVERT: A 401 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8510 (mtpp) REVERT: C 60 ASP cc_start: 0.8149 (t70) cc_final: 0.7178 (t0) REVERT: C 100 MET cc_start: 0.8096 (mmm) cc_final: 0.7857 (mmp) REVERT: C 119 MET cc_start: 0.8772 (ttp) cc_final: 0.8347 (ttp) REVERT: C 150 LYS cc_start: 0.9025 (mttm) cc_final: 0.8738 (tptt) REVERT: C 248 ASP cc_start: 0.7881 (m-30) cc_final: 0.7425 (m-30) REVERT: C 270 ASP cc_start: 0.8396 (m-30) cc_final: 0.7835 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7379 (t0) cc_final: 0.6884 (m-30) REVERT: C 300 ASP cc_start: 0.8629 (t70) cc_final: 0.7631 (t0) REVERT: C 368 LYS cc_start: 0.8823 (mttm) cc_final: 0.8569 (ptmm) REVERT: C 591 ARG cc_start: 0.5923 (mpt180) cc_final: 0.5723 (mpp-170) REVERT: D 17 THR cc_start: 0.9279 (m) cc_final: 0.8977 (t) REVERT: D 20 LYS cc_start: 0.8030 (tttm) cc_final: 0.7630 (tppt) REVERT: D 104 ASP cc_start: 0.8186 (t0) cc_final: 0.7560 (t0) REVERT: D 117 ASP cc_start: 0.7459 (t0) cc_final: 0.6961 (t70) REVERT: D 144 LYS cc_start: 0.7790 (tptm) cc_final: 0.7574 (tptm) REVERT: D 162 SER cc_start: 0.8061 (t) cc_final: 0.7749 (p) REVERT: E 35 ASP cc_start: 0.8363 (m-30) cc_final: 0.8020 (m-30) REVERT: E 59 ASN cc_start: 0.7870 (t0) cc_final: 0.7322 (t0) REVERT: E 83 GLU cc_start: 0.8362 (pm20) cc_final: 0.7902 (pm20) REVERT: E 163 ASP cc_start: 0.8768 (m-30) cc_final: 0.8544 (p0) REVERT: E 247 ASP cc_start: 0.8284 (m-30) cc_final: 0.8007 (t0) REVERT: E 280 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6059 (mp) REVERT: E 309 LEU cc_start: 0.8911 (mp) cc_final: 0.8217 (tt) REVERT: E 425 PHE cc_start: 0.8876 (m-80) cc_final: 0.8591 (m-80) REVERT: E 455 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7862 (pmm-80) REVERT: E 456 ASP cc_start: 0.8743 (m-30) cc_final: 0.8388 (m-30) REVERT: E 458 LEU cc_start: 0.9279 (mt) cc_final: 0.9025 (tm) REVERT: E 478 PHE cc_start: 0.8420 (m-10) cc_final: 0.7860 (m-80) outliers start: 57 outliers final: 28 residues processed: 267 average time/residue: 0.9950 time to fit residues: 307.4564 Evaluate side-chains 236 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 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 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 459 VAL Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 455 ARG Chi-restraints excluded: chain E residue 515 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS C 82 GLN C 235 GLN D 88 GLN D 101 ASN E 165 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18597 Z= 0.245 Angle : 0.634 16.321 25180 Z= 0.312 Chirality : 0.043 0.227 2772 Planarity : 0.004 0.061 3187 Dihedral : 5.113 74.786 2400 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.86 % Rotamer: Outliers : 2.51 % Allowed : 17.74 % Favored : 79.75 % 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: -0.08 (0.18), residues: 2166 helix: 1.13 (0.15), residues: 1293 sheet: -1.47 (0.76), residues: 46 loop : -1.94 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 150 HIS 0.004 0.001 HIS D 96 PHE 0.017 0.001 PHE B 2 TYR 0.030 0.001 TYR C 237 ARG 0.014 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 212 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7659 (mtm180) REVERT: B 60 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: B 135 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: B 139 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7155 (mpt-90) REVERT: B 146 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7431 (mtp180) REVERT: B 279 ASP cc_start: 0.6922 (t0) cc_final: 0.6532 (t0) REVERT: B 291 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6795 (mtm110) REVERT: B 345 TYR cc_start: 0.8036 (t80) cc_final: 0.7811 (t80) REVERT: B 550 LEU cc_start: 0.8590 (tp) cc_final: 0.8336 (mm) REVERT: B 560 LYS cc_start: 0.8346 (mttt) cc_final: 0.8003 (mmmt) REVERT: A 11 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8241 (mt-10) REVERT: A 64 ARG cc_start: 0.8656 (ttt180) cc_final: 0.8391 (mtp85) REVERT: A 78 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 119 GLU cc_start: 0.7676 (tt0) cc_final: 0.7166 (tt0) REVERT: A 163 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7920 (mm) REVERT: A 175 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6893 (pp) REVERT: A 275 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6327 (tptm) REVERT: A 282 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7908 (tttm) REVERT: A 302 SER cc_start: 0.7846 (t) cc_final: 0.7579 (t) REVERT: A 310 ASN cc_start: 0.7276 (t0) cc_final: 0.6883 (m-40) REVERT: A 354 LYS cc_start: 0.8782 (tppt) cc_final: 0.8470 (pttp) REVERT: A 355 ASN cc_start: 0.8509 (t0) cc_final: 0.8177 (m-40) REVERT: A 395 ASP cc_start: 0.6975 (t0) cc_final: 0.6656 (t0) REVERT: A 400 THR cc_start: 0.9172 (m) cc_final: 0.8926 (p) REVERT: A 401 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8552 (mtpp) REVERT: A 412 GLU cc_start: 0.6606 (tt0) cc_final: 0.6364 (tt0) REVERT: A 447 GLU cc_start: 0.7453 (tt0) cc_final: 0.6809 (tp30) REVERT: C 60 ASP cc_start: 0.8180 (t70) cc_final: 0.7209 (t0) REVERT: C 100 MET cc_start: 0.8136 (mmm) cc_final: 0.7901 (mmp) REVERT: C 119 MET cc_start: 0.8739 (ttp) cc_final: 0.8299 (ttp) REVERT: C 150 LYS cc_start: 0.9023 (mttm) cc_final: 0.8761 (tptt) REVERT: C 248 ASP cc_start: 0.7917 (m-30) cc_final: 0.7445 (m-30) REVERT: C 270 ASP cc_start: 0.8413 (m-30) cc_final: 0.7836 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7460 (t0) cc_final: 0.6955 (m-30) REVERT: C 300 ASP cc_start: 0.8488 (t70) cc_final: 0.7561 (t0) REVERT: C 368 LYS cc_start: 0.8833 (mttm) cc_final: 0.8583 (ptmm) REVERT: D 17 THR cc_start: 0.9268 (m) cc_final: 0.8956 (t) REVERT: D 20 LYS cc_start: 0.8116 (tttm) cc_final: 0.7698 (tppt) REVERT: D 104 ASP cc_start: 0.8143 (t0) cc_final: 0.7642 (t0) REVERT: D 117 ASP cc_start: 0.7452 (t0) cc_final: 0.6946 (t70) REVERT: D 162 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7739 (p) REVERT: E 35 ASP cc_start: 0.8352 (m-30) cc_final: 0.8007 (m-30) REVERT: E 59 ASN cc_start: 0.7804 (t0) cc_final: 0.7175 (t0) REVERT: E 83 GLU cc_start: 0.8348 (pm20) cc_final: 0.7809 (pm20) REVERT: E 163 ASP cc_start: 0.8787 (m-30) cc_final: 0.8543 (p0) REVERT: E 247 ASP cc_start: 0.8279 (m-30) cc_final: 0.7992 (t0) REVERT: E 280 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6019 (mp) REVERT: E 309 LEU cc_start: 0.8917 (mp) cc_final: 0.8251 (tt) REVERT: E 336 GLU cc_start: 0.8719 (mp0) cc_final: 0.8330 (pm20) REVERT: E 425 PHE cc_start: 0.8866 (m-80) cc_final: 0.8580 (m-80) REVERT: E 455 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7871 (pmm-80) REVERT: E 456 ASP cc_start: 0.8676 (m-30) cc_final: 0.8316 (m-30) REVERT: E 458 LEU cc_start: 0.9258 (mt) cc_final: 0.9007 (tm) REVERT: E 478 PHE cc_start: 0.8506 (m-10) cc_final: 0.7919 (m-80) outliers start: 51 outliers final: 27 residues processed: 250 average time/residue: 1.0660 time to fit residues: 306.6114 Evaluate side-chains 234 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 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 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 377 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 455 ARG Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 515 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.0870 chunk 125 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 136 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS C 82 GLN C 235 GLN C 474 GLN D 88 GLN D 101 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18597 Z= 0.190 Angle : 0.627 16.073 25180 Z= 0.305 Chirality : 0.042 0.232 2772 Planarity : 0.004 0.061 3187 Dihedral : 5.062 75.056 2400 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 1.97 % Allowed : 18.43 % Favored : 79.61 % 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: 0.03 (0.18), residues: 2166 helix: 1.21 (0.15), residues: 1293 sheet: -1.43 (0.66), residues: 56 loop : -1.89 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 150 HIS 0.003 0.001 HIS D 96 PHE 0.024 0.001 PHE E 468 TYR 0.026 0.001 TYR E 49 ARG 0.015 0.000 ARG A 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7718 (mtm180) REVERT: B 60 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: B 135 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: B 139 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7157 (mpt-90) REVERT: B 146 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7393 (mtp180) REVERT: B 279 ASP cc_start: 0.6906 (t0) cc_final: 0.6516 (t0) REVERT: B 291 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6794 (mtm110) REVERT: B 345 TYR cc_start: 0.8064 (t80) cc_final: 0.7826 (t80) REVERT: B 550 LEU cc_start: 0.8591 (tp) cc_final: 0.8340 (mm) REVERT: B 560 LYS cc_start: 0.8354 (mttt) cc_final: 0.8018 (mmmt) REVERT: B 591 ARG cc_start: 0.7348 (mtt-85) cc_final: 0.6879 (ttm110) REVERT: A 11 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8205 (mt-10) REVERT: A 46 GLU cc_start: 0.8950 (tp30) cc_final: 0.8524 (mm-30) REVERT: A 64 ARG cc_start: 0.8671 (ttt180) cc_final: 0.8413 (mtp85) REVERT: A 78 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 119 GLU cc_start: 0.7732 (tt0) cc_final: 0.7215 (tt0) REVERT: A 163 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 175 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6688 (pp) REVERT: A 275 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6327 (tptm) REVERT: A 282 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7898 (tttm) REVERT: A 302 SER cc_start: 0.7872 (t) cc_final: 0.7419 (p) REVERT: A 310 ASN cc_start: 0.7249 (t0) cc_final: 0.6872 (m-40) REVERT: A 333 ASN cc_start: 0.8645 (t0) cc_final: 0.8330 (m-40) REVERT: A 354 LYS cc_start: 0.8761 (tppt) cc_final: 0.8491 (pttp) REVERT: A 355 ASN cc_start: 0.8479 (t0) cc_final: 0.8159 (m-40) REVERT: A 394 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 400 THR cc_start: 0.9146 (m) cc_final: 0.8885 (p) REVERT: A 401 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8452 (mtpp) REVERT: C 60 ASP cc_start: 0.8170 (t70) cc_final: 0.7203 (t0) REVERT: C 100 MET cc_start: 0.8117 (mmm) cc_final: 0.7890 (mmp) REVERT: C 119 MET cc_start: 0.8732 (ttp) cc_final: 0.8292 (ttp) REVERT: C 150 LYS cc_start: 0.9021 (mttm) cc_final: 0.8748 (tptt) REVERT: C 248 ASP cc_start: 0.7910 (m-30) cc_final: 0.7438 (m-30) REVERT: C 270 ASP cc_start: 0.8411 (m-30) cc_final: 0.7833 (OUTLIER) REVERT: C 279 ASP cc_start: 0.7526 (t0) cc_final: 0.7008 (m-30) REVERT: C 300 ASP cc_start: 0.8364 (t70) cc_final: 0.7443 (t0) REVERT: C 368 LYS cc_start: 0.8863 (mttm) cc_final: 0.8562 (ptmm) REVERT: D 17 THR cc_start: 0.9252 (m) cc_final: 0.8935 (t) REVERT: D 20 LYS cc_start: 0.8074 (tttm) cc_final: 0.7628 (tppt) REVERT: D 104 ASP cc_start: 0.8074 (t0) cc_final: 0.7370 (t0) REVERT: D 117 ASP cc_start: 0.7423 (t0) cc_final: 0.6929 (t70) REVERT: D 162 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7751 (p) REVERT: E 35 ASP cc_start: 0.8367 (m-30) cc_final: 0.8024 (m-30) REVERT: E 59 ASN cc_start: 0.7772 (t0) cc_final: 0.7282 (t0) REVERT: E 83 GLU cc_start: 0.8329 (pm20) cc_final: 0.7827 (pm20) REVERT: E 163 ASP cc_start: 0.8775 (m-30) cc_final: 0.8523 (p0) REVERT: E 247 ASP cc_start: 0.8292 (m-30) cc_final: 0.7991 (t0) REVERT: E 309 LEU cc_start: 0.8915 (mp) cc_final: 0.8255 (tt) REVERT: E 336 GLU cc_start: 0.8706 (mp0) cc_final: 0.8325 (pm20) REVERT: E 407 MET cc_start: 0.7790 (mmm) cc_final: 0.7387 (mtp) REVERT: E 425 PHE cc_start: 0.8862 (m-80) cc_final: 0.8606 (m-80) REVERT: E 455 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7868 (pmm-80) REVERT: E 456 ASP cc_start: 0.8678 (m-30) cc_final: 0.8303 (m-30) REVERT: E 458 LEU cc_start: 0.9255 (mt) cc_final: 0.9010 (tm) REVERT: E 478 PHE cc_start: 0.8500 (m-10) cc_final: 0.7923 (m-80) REVERT: E 515 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7409 (t0) outliers start: 40 outliers final: 26 residues processed: 245 average time/residue: 1.1277 time to fit residues: 319.8792 Evaluate side-chains 238 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 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 360 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 455 ARG Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 515 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 158 optimal weight: 0.0170 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 177 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN A 439 HIS C 82 GLN C 235 GLN D 101 ASN E 191 ASN ** E 283 GLN ** 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 = 0.3770 r_free = 0.3770 target = 0.132677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091744 restraints weight = 28692.424| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.79 r_work: 0.3014 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18597 Z= 0.159 Angle : 0.613 15.887 25180 Z= 0.297 Chirality : 0.041 0.231 2772 Planarity : 0.004 0.062 3187 Dihedral : 4.965 75.766 2400 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 1.62 % Allowed : 19.36 % Favored : 79.02 % 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: 0.20 (0.19), residues: 2166 helix: 1.37 (0.15), residues: 1287 sheet: -1.30 (0.66), residues: 56 loop : -1.85 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 150 HIS 0.003 0.001 HIS D 96 PHE 0.013 0.001 PHE C 101 TYR 0.026 0.001 TYR E 49 ARG 0.015 0.000 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6239.71 seconds wall clock time: 111 minutes 27.39 seconds (6687.39 seconds total)