Starting phenix.real_space_refine on Fri Feb 16 10:09:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/02_2024/8or4_17117.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/02_2024/8or4_17117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/02_2024/8or4_17117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/02_2024/8or4_17117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/02_2024/8or4_17117.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/02_2024/8or4_17117.pdb" } resolution = 3.8 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 85 5.16 5 C 9526 2.51 5 N 2557 2.21 5 O 2868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 18": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 915": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15036 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5231 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 11, 'TRANS': 644} Chain breaks: 7 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 9, 'PHE:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 6347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6347 Classifications: {'peptide': 843} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 37, 'TRANS': 805} Chain breaks: 11 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 7, 'ASP:plan': 4, 'PHE:plan': 2, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1616 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 5 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 303 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 153 Chain: "H" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 244 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 43} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 111 Time building chain proxies: 8.55, per 1000 atoms: 0.57 Number of scatterers: 15036 At special positions: 0 Unit cell: (126.36, 179.28, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 85 16.00 O 2868 8.00 N 2557 7.00 C 9526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.83 Conformation dependent library (CDL) restraints added in 2.8 seconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 4 sheets defined 66.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.529A pdb=" N GLY A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.965A pdb=" N HIS A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 107 removed outlier: 3.636A pdb=" N ARG A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 3.853A pdb=" N THR A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.540A pdb=" N ASP A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.993A pdb=" N GLN A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 225 through 255 removed outlier: 5.382A pdb=" N SER A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.953A pdb=" N MET A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 296 removed outlier: 3.727A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 4.091A pdb=" N GLN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 332 through 356 removed outlier: 4.607A pdb=" N LEU A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.762A pdb=" N LEU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.833A pdb=" N ASN A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.666A pdb=" N MET A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.584A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.941A pdb=" N TYR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.888A pdb=" N HIS A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 496 Processing helix chain 'A' and resid 497 through 528 removed outlier: 3.862A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 removed outlier: 4.003A pdb=" N ARG A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.695A pdb=" N LEU A 612 " --> pdb=" O MET A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 630 removed outlier: 4.098A pdb=" N ASP A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 628 " --> pdb=" O GLN A 624 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 629 " --> pdb=" O LEU A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 646 removed outlier: 3.523A pdb=" N SER A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 722 removed outlier: 3.864A pdb=" N GLN A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.699A pdb=" N LEU A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.864A pdb=" N THR B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 16 removed outlier: 4.166A pdb=" N LEU C 11 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU C 12 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 36 removed outlier: 3.738A pdb=" N ARG C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.940A pdb=" N GLN C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.908A pdb=" N MET C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.563A pdb=" N SER C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 139 Processing helix chain 'C' and resid 140 through 143 Processing helix chain 'C' and resid 148 through 165 removed outlier: 3.848A pdb=" N LEU C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.546A pdb=" N VAL C 170 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN C 171 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.889A pdb=" N ILE C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 removed outlier: 4.147A pdb=" N THR C 185 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 removed outlier: 3.698A pdb=" N CYS C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.930A pdb=" N GLU C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.649A pdb=" N SER C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 265 removed outlier: 4.169A pdb=" N GLU C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.144A pdb=" N ASN C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 285 removed outlier: 3.702A pdb=" N CYS C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 303 removed outlier: 4.302A pdb=" N LYS C 303 " --> pdb=" O ASN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 removed outlier: 4.021A pdb=" N ARG C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 removed outlier: 4.765A pdb=" N ALA C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.903A pdb=" N ALA C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 443 removed outlier: 4.374A pdb=" N MET C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Proline residue: C 433 - end of helix removed outlier: 3.913A pdb=" N LYS C 441 " --> pdb=" O LYS C 437 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET C 443 " --> pdb=" O LEU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 465 removed outlier: 4.044A pdb=" N ARG C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 486 Proline residue: C 478 - end of helix Processing helix chain 'C' and resid 490 through 507 removed outlier: 4.026A pdb=" N ASN C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 516 through 528 Proline residue: C 522 - end of helix Processing helix chain 'C' and resid 532 through 549 removed outlier: 3.705A pdb=" N THR C 536 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 577 removed outlier: 4.280A pdb=" N LYS C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP C 567 " --> pdb=" O PRO C 563 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 601 Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.538A pdb=" N GLY C 605 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER C 606 " --> pdb=" O ASN C 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 606' Processing helix chain 'C' and resid 607 through 621 removed outlier: 3.830A pdb=" N LYS C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 644 through 650 Processing helix chain 'C' and resid 651 through 657 Processing helix chain 'C' and resid 666 through 677 removed outlier: 3.878A pdb=" N LEU C 671 " --> pdb=" O LYS C 667 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.633A pdb=" N ALA C 687 " --> pdb=" O SER C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.899A pdb=" N ASP C 695 " --> pdb=" O ASP C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 701 Proline residue: C 699 - end of helix No H-bonds generated for 'chain 'C' and resid 696 through 701' Processing helix chain 'C' and resid 702 through 720 removed outlier: 4.428A pdb=" N VAL C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 711 " --> pdb=" O HIS C 707 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 719 " --> pdb=" O PHE C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 743 Processing helix chain 'C' and resid 758 through 762 Processing helix chain 'C' and resid 763 through 768 Processing helix chain 'C' and resid 789 through 806 removed outlier: 3.591A pdb=" N SER C 795 " --> pdb=" O THR C 791 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 806 " --> pdb=" O CYS C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 827 through 836 removed outlier: 3.610A pdb=" N THR C 831 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 877 removed outlier: 4.280A pdb=" N ALA C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.667A pdb=" N ASN C 887 " --> pdb=" O SER C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 917 removed outlier: 3.836A pdb=" N LYS C 914 " --> pdb=" O LEU C 910 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 917 " --> pdb=" O LEU C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 933 removed outlier: 4.148A pdb=" N ILE C 932 " --> pdb=" O TYR C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 953 Processing helix chain 'D' and resid 20 through 23 Processing helix chain 'D' and resid 24 through 33 removed outlier: 4.501A pdb=" N MET D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.016A pdb=" N HIS D 65 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS D 66 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 67 " --> pdb=" O HIS D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 67' Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.949A pdb=" N GLN D 96 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 98 " --> pdb=" O TRP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.928A pdb=" N GLU D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASN D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 137 through 144 removed outlier: 4.748A pdb=" N ARG D 142 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.851A pdb=" N LEU E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 124 through 132 removed outlier: 3.674A pdb=" N ARG E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER E 132 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 159 removed outlier: 3.576A pdb=" N THR E 152 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 219 through 229 removed outlier: 4.077A pdb=" N ILE E 222 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASN E 224 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 226 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS E 228 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 255 Processing helix chain 'G' and resid 25 through 32 removed outlier: 3.816A pdb=" N LYS G 30 " --> pdb=" O LYS G 26 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 31 " --> pdb=" O ASP G 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 188 Processing helix chain 'H' and resid 208 through 218 removed outlier: 4.064A pdb=" N ARG H 214 " --> pdb=" O ASP H 210 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE H 215 " --> pdb=" O GLN H 211 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 539 removed outlier: 6.299A pdb=" N GLN A 538 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.650A pdb=" N ILE D 4 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 16 " --> pdb=" O ILE D 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AA4, first strand: chain 'E' and resid 185 through 189 removed outlier: 3.570A pdb=" N SER E 212 " --> pdb=" O MET E 186 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2121 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: 3.88 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2721 1.33 - 1.45: 3439 1.45 - 1.57: 8954 1.57 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 15236 Sorted by residual: bond pdb=" CA GLN C 854 " pdb=" C GLN C 854 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.32e-02 5.74e+03 1.45e+01 bond pdb=" N GLN C 854 " pdb=" CA GLN C 854 " ideal model delta sigma weight residual 1.459 1.417 0.042 1.20e-02 6.94e+03 1.24e+01 bond pdb=" C GLN C 854 " pdb=" O GLN C 854 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.15e-02 7.56e+03 9.02e+00 bond pdb=" CA GLN C 854 " pdb=" CB GLN C 854 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.56e-02 4.11e+03 5.50e+00 bond pdb=" N GLU C 856 " pdb=" CA GLU C 856 " ideal model delta sigma weight residual 1.456 1.428 0.027 1.26e-02 6.30e+03 4.62e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.27: 415 107.27 - 113.97: 8946 113.97 - 120.68: 6407 120.68 - 127.38: 4745 127.38 - 134.09: 126 Bond angle restraints: 20639 Sorted by residual: angle pdb=" N GLN C 854 " pdb=" CA GLN C 854 " pdb=" C GLN C 854 " ideal model delta sigma weight residual 111.11 117.41 -6.30 1.20e+00 6.94e-01 2.76e+01 angle pdb=" CA ARG E 415 " pdb=" CB ARG E 415 " pdb=" CG ARG E 415 " ideal model delta sigma weight residual 114.10 123.73 -9.63 2.00e+00 2.50e-01 2.32e+01 angle pdb=" N SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta sigma weight residual 110.65 103.74 6.91 1.58e+00 4.01e-01 1.91e+01 angle pdb=" N GLU C 856 " pdb=" CA GLU C 856 " pdb=" CB GLU C 856 " ideal model delta sigma weight residual 110.56 104.44 6.12 1.46e+00 4.69e-01 1.76e+01 angle pdb=" C SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta sigma weight residual 110.74 104.38 6.36 1.61e+00 3.86e-01 1.56e+01 ... (remaining 20634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8157 17.91 - 35.81: 906 35.81 - 53.72: 229 53.72 - 71.63: 37 71.63 - 89.53: 14 Dihedral angle restraints: 9343 sinusoidal: 3508 harmonic: 5835 Sorted by residual: dihedral pdb=" CA ARG C 664 " pdb=" C ARG C 664 " pdb=" N ALA C 665 " pdb=" CA ALA C 665 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU C 925 " pdb=" C LEU C 925 " pdb=" N LYS C 926 " pdb=" CA LYS C 926 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" N SER C 852 " pdb=" C SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta harmonic sigma weight residual 122.80 112.77 10.03 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 9340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2364 0.071 - 0.143: 143 0.143 - 0.214: 0 0.214 - 0.285: 1 0.285 - 0.357: 4 Chirality restraints: 2512 Sorted by residual: chirality pdb=" CA ARG A 561 " pdb=" N ARG A 561 " pdb=" C ARG A 561 " pdb=" CB ARG A 561 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA ARG E 294 " pdb=" N ARG E 294 " pdb=" C ARG E 294 " pdb=" CB ARG E 294 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA GLN C 854 " pdb=" N GLN C 854 " pdb=" C GLN C 854 " pdb=" CB GLN C 854 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2509 not shown) Planarity restraints: 2611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 625 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ARG C 625 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG C 625 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU C 626 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 698 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO C 699 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 699 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 699 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 853 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C GLY C 853 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY C 853 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C 854 " 0.014 2.00e-02 2.50e+03 ... (remaining 2608 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 122 2.52 - 3.12: 12505 3.12 - 3.71: 22644 3.71 - 4.31: 28014 4.31 - 4.90: 46238 Nonbonded interactions: 109523 Sorted by model distance: nonbonded pdb=" O LYS C 914 " pdb=" OG SER C 918 " model vdw 1.930 2.440 nonbonded pdb=" OH TYR C 372 " pdb=" OG1 THR C 405 " model vdw 1.994 2.440 nonbonded pdb=" OD2 ASP A 427 " pdb=" CG MET A 469 " model vdw 2.012 3.440 nonbonded pdb=" NZ LYS C 667 " pdb=" OD1 ASP C 705 " model vdw 2.017 2.520 nonbonded pdb=" O PHE C 371 " pdb=" OG1 THR C 374 " model vdw 2.019 2.440 ... (remaining 109518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.220 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 39.530 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 : 0.003 0.050 15236 Z= 0.176 Angle : 0.588 9.639 20639 Z= 0.307 Chirality : 0.037 0.357 2512 Planarity : 0.004 0.072 2611 Dihedral : 16.205 89.532 5503 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.31 % Allowed : 24.89 % Favored : 74.80 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1914 helix: 1.35 (0.17), residues: 1026 sheet: 0.42 (1.35), residues: 21 loop : -1.68 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 123 HIS 0.002 0.000 HIS A 343 PHE 0.020 0.001 PHE A 402 TYR 0.012 0.001 TYR A 99 ARG 0.007 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 355 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8648 (tttt) cc_final: 0.7986 (tptp) REVERT: A 139 TYR cc_start: 0.7543 (t80) cc_final: 0.7310 (t80) REVERT: A 196 ILE cc_start: 0.7739 (mt) cc_final: 0.7328 (mm) REVERT: A 242 ARG cc_start: 0.7568 (ptt90) cc_final: 0.7322 (ptt90) REVERT: A 271 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 315 LYS cc_start: 0.6995 (mmtm) cc_final: 0.6676 (mmmm) REVERT: A 377 TYR cc_start: 0.8109 (m-80) cc_final: 0.7563 (m-80) REVERT: A 451 VAL cc_start: 0.7904 (t) cc_final: 0.7644 (t) REVERT: A 501 THR cc_start: 0.6782 (m) cc_final: 0.5522 (t) REVERT: A 509 GLN cc_start: 0.6005 (tp-100) cc_final: 0.5745 (tp-100) REVERT: A 627 ASP cc_start: 0.7569 (m-30) cc_final: 0.7228 (m-30) REVERT: C 25 MET cc_start: 0.7169 (mmm) cc_final: 0.6659 (mmm) REVERT: C 63 GLU cc_start: 0.8535 (tt0) cc_final: 0.7720 (tp30) REVERT: C 158 MET cc_start: 0.7309 (ttp) cc_final: 0.6976 (ttp) REVERT: C 234 TYR cc_start: 0.6864 (m-80) cc_final: 0.6475 (m-80) REVERT: C 451 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7127 (mtt180) REVERT: C 593 MET cc_start: 0.8058 (tpp) cc_final: 0.7568 (tpp) REVERT: C 679 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7962 (ttmt) REVERT: C 793 LYS cc_start: 0.7957 (mttp) cc_final: 0.7733 (mttm) outliers start: 5 outliers final: 2 residues processed: 359 average time/residue: 0.2704 time to fit residues: 143.1235 Evaluate side-chains 335 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 333 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain E residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.0670 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.0470 chunk 100 optimal weight: 0.0570 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 0.0770 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS A 700 HIS C 299 ASN C 514 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15236 Z= 0.188 Angle : 0.651 11.268 20639 Z= 0.322 Chirality : 0.039 0.204 2512 Planarity : 0.004 0.065 2611 Dihedral : 4.192 27.354 2061 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.68 % Allowed : 22.96 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1914 helix: 1.20 (0.16), residues: 1073 sheet: 2.76 (1.40), residues: 11 loop : -1.82 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 123 HIS 0.005 0.001 HIS C 173 PHE 0.026 0.001 PHE A 498 TYR 0.013 0.001 TYR A 278 ARG 0.009 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 363 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7236 (tp) cc_final: 0.6598 (tp) REVERT: A 117 LYS cc_start: 0.8622 (tttt) cc_final: 0.8017 (tptp) REVERT: A 123 TRP cc_start: 0.7065 (t60) cc_final: 0.6718 (t60) REVERT: A 196 ILE cc_start: 0.7802 (mt) cc_final: 0.7347 (mm) REVERT: A 290 LYS cc_start: 0.8262 (ptmt) cc_final: 0.8032 (ptmm) REVERT: A 315 LYS cc_start: 0.7262 (mmtm) cc_final: 0.6902 (mmmm) REVERT: A 335 GLU cc_start: 0.7336 (tp30) cc_final: 0.6989 (tp30) REVERT: A 377 TYR cc_start: 0.8202 (m-80) cc_final: 0.7647 (m-80) REVERT: A 451 VAL cc_start: 0.8034 (t) cc_final: 0.7772 (t) REVERT: A 469 MET cc_start: 0.6771 (tpp) cc_final: 0.6557 (tpp) REVERT: A 501 THR cc_start: 0.7086 (m) cc_final: 0.5770 (t) REVERT: A 509 GLN cc_start: 0.6107 (tp-100) cc_final: 0.5835 (tp-100) REVERT: A 627 ASP cc_start: 0.7468 (m-30) cc_final: 0.7122 (m-30) REVERT: A 711 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7363 (pt) REVERT: C 15 MET cc_start: 0.7651 (tpp) cc_final: 0.7271 (tpp) REVERT: C 25 MET cc_start: 0.6945 (mmm) cc_final: 0.6361 (mmm) REVERT: C 53 ILE cc_start: 0.7306 (tp) cc_final: 0.6768 (pt) REVERT: C 70 LYS cc_start: 0.8300 (mttt) cc_final: 0.8070 (mttt) REVERT: C 132 LYS cc_start: 0.8408 (mttt) cc_final: 0.8206 (mttt) REVERT: C 157 ILE cc_start: 0.8251 (tp) cc_final: 0.7562 (tp) REVERT: C 161 MET cc_start: 0.6827 (mpp) cc_final: 0.6533 (mpp) REVERT: C 192 ARG cc_start: 0.8460 (mtm180) cc_final: 0.8116 (mtm-85) REVERT: C 221 GLU cc_start: 0.7830 (tp30) cc_final: 0.7565 (tp30) REVERT: C 254 GLU cc_start: 0.7362 (mp0) cc_final: 0.6808 (mp0) REVERT: C 469 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6716 (tp) REVERT: C 494 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7369 (mmtt) REVERT: C 569 PHE cc_start: 0.7472 (t80) cc_final: 0.7269 (t80) REVERT: C 593 MET cc_start: 0.7960 (tpp) cc_final: 0.7579 (tpp) REVERT: C 679 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7934 (ttmt) REVERT: C 690 ILE cc_start: 0.6643 (mt) cc_final: 0.6365 (mm) REVERT: C 793 LYS cc_start: 0.7996 (mttp) cc_final: 0.7694 (mttm) REVERT: C 802 CYS cc_start: 0.6972 (m) cc_final: 0.6119 (t) REVERT: C 916 ILE cc_start: 0.8760 (pt) cc_final: 0.7937 (pt) REVERT: E 222 ILE cc_start: 0.8108 (tp) cc_final: 0.7795 (tp) outliers start: 59 outliers final: 29 residues processed: 394 average time/residue: 0.2634 time to fit residues: 152.4288 Evaluate side-chains 379 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 607 ASP Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 0.0270 chunk 121 optimal weight: 0.0170 chunk 49 optimal weight: 5.9990 chunk 178 optimal weight: 0.4980 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 284 GLN A 368 GLN A 641 GLN A 700 HIS C 299 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15236 Z= 0.172 Angle : 0.626 10.524 20639 Z= 0.305 Chirality : 0.039 0.198 2512 Planarity : 0.004 0.062 2611 Dihedral : 4.075 22.054 2057 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.24 % Allowed : 23.08 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1914 helix: 1.29 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -1.72 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 123 HIS 0.005 0.001 HIS C 173 PHE 0.024 0.001 PHE A 402 TYR 0.020 0.001 TYR A 260 ARG 0.008 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 363 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7133 (tp) cc_final: 0.6796 (tp) REVERT: A 117 LYS cc_start: 0.8622 (tttt) cc_final: 0.7999 (tptp) REVERT: A 196 ILE cc_start: 0.7832 (mt) cc_final: 0.7359 (mm) REVERT: A 235 GLN cc_start: 0.7178 (mp10) cc_final: 0.6840 (mp10) REVERT: A 242 ARG cc_start: 0.7319 (ptt90) cc_final: 0.6617 (ptt90) REVERT: A 281 GLU cc_start: 0.7307 (tp30) cc_final: 0.7009 (tp30) REVERT: A 290 LYS cc_start: 0.8113 (ptmt) cc_final: 0.7772 (ptmm) REVERT: A 303 PHE cc_start: 0.7090 (m-10) cc_final: 0.6869 (m-80) REVERT: A 315 LYS cc_start: 0.7354 (mmtm) cc_final: 0.7031 (mmmm) REVERT: A 330 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 331 ASP cc_start: 0.7154 (t0) cc_final: 0.6734 (t0) REVERT: A 377 TYR cc_start: 0.8246 (m-80) cc_final: 0.7753 (m-80) REVERT: A 451 VAL cc_start: 0.7914 (t) cc_final: 0.7660 (t) REVERT: A 498 PHE cc_start: 0.7038 (t80) cc_final: 0.6723 (t80) REVERT: A 501 THR cc_start: 0.7255 (m) cc_final: 0.5899 (t) REVERT: A 509 GLN cc_start: 0.6116 (tp-100) cc_final: 0.5879 (tp-100) REVERT: A 627 ASP cc_start: 0.7437 (m-30) cc_final: 0.7091 (m-30) REVERT: A 705 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7043 (mm-30) REVERT: C 15 MET cc_start: 0.7561 (tpp) cc_final: 0.7350 (tpp) REVERT: C 48 LYS cc_start: 0.8242 (mttp) cc_final: 0.7987 (mttp) REVERT: C 53 ILE cc_start: 0.7170 (tp) cc_final: 0.6672 (pt) REVERT: C 70 LYS cc_start: 0.8254 (mttt) cc_final: 0.7996 (mttt) REVERT: C 157 ILE cc_start: 0.8370 (tp) cc_final: 0.8021 (tp) REVERT: C 161 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6539 (mpp) REVERT: C 192 ARG cc_start: 0.8440 (mtm180) cc_final: 0.8106 (mtm-85) REVERT: C 221 GLU cc_start: 0.7870 (tp30) cc_final: 0.7552 (tp30) REVERT: C 451 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7333 (mtt180) REVERT: C 469 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6741 (tp) REVERT: C 494 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7396 (mmtt) REVERT: C 569 PHE cc_start: 0.7592 (t80) cc_final: 0.7383 (t80) REVERT: C 593 MET cc_start: 0.7955 (tpp) cc_final: 0.7504 (tpp) REVERT: C 628 THR cc_start: 0.7782 (m) cc_final: 0.7540 (p) REVERT: C 643 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.6972 (p0) REVERT: C 668 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7564 (tm) REVERT: C 679 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7964 (ttmt) REVERT: C 690 ILE cc_start: 0.6778 (mt) cc_final: 0.6384 (mm) REVERT: C 693 VAL cc_start: 0.7886 (t) cc_final: 0.7298 (p) REVERT: C 777 ARG cc_start: 0.8323 (mmm160) cc_final: 0.8090 (mmp80) REVERT: C 793 LYS cc_start: 0.7972 (mttp) cc_final: 0.7612 (mttm) REVERT: C 802 CYS cc_start: 0.6849 (m) cc_final: 0.6102 (t) REVERT: C 915 GLU cc_start: 0.8600 (pp20) cc_final: 0.8105 (pp20) REVERT: D 132 MET cc_start: 0.7264 (mtt) cc_final: 0.7000 (mpp) REVERT: E 222 ILE cc_start: 0.8172 (tp) cc_final: 0.7890 (tp) REVERT: E 418 LEU cc_start: 0.4505 (tp) cc_final: 0.4185 (tp) outliers start: 68 outliers final: 33 residues processed: 401 average time/residue: 0.2594 time to fit residues: 154.7032 Evaluate side-chains 387 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 350 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 757 ASP Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 85 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 178 GLN ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 505 GLN A 700 HIS C 265 ASN C 299 ASN ** C 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15236 Z= 0.206 Angle : 0.645 10.326 20639 Z= 0.314 Chirality : 0.040 0.213 2512 Planarity : 0.004 0.058 2611 Dihedral : 4.237 22.131 2057 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.43 % Allowed : 23.96 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1914 helix: 1.14 (0.16), residues: 1081 sheet: -3.59 (1.11), residues: 10 loop : -1.81 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 137 HIS 0.005 0.001 HIS C 508 PHE 0.023 0.001 PHE A 402 TYR 0.016 0.001 TYR A 278 ARG 0.008 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 357 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.7479 (m-40) cc_final: 0.7236 (m-40) REVERT: A 104 LEU cc_start: 0.7167 (tp) cc_final: 0.6677 (tp) REVERT: A 117 LYS cc_start: 0.8670 (tttt) cc_final: 0.7994 (tptp) REVERT: A 263 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8620 (ttpp) REVERT: A 281 GLU cc_start: 0.7428 (tp30) cc_final: 0.7140 (tp30) REVERT: A 290 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7814 (ptmm) REVERT: A 315 LYS cc_start: 0.7574 (mmtm) cc_final: 0.7177 (mmmm) REVERT: A 331 ASP cc_start: 0.7168 (t0) cc_final: 0.6815 (t0) REVERT: A 377 TYR cc_start: 0.8394 (m-80) cc_final: 0.7893 (m-80) REVERT: A 451 VAL cc_start: 0.7848 (t) cc_final: 0.7601 (t) REVERT: A 627 ASP cc_start: 0.7443 (m-30) cc_final: 0.7104 (m-30) REVERT: A 705 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7022 (mm-30) REVERT: C 15 MET cc_start: 0.7598 (tpp) cc_final: 0.7386 (tpp) REVERT: C 29 ASP cc_start: 0.7722 (p0) cc_final: 0.7403 (m-30) REVERT: C 48 LYS cc_start: 0.8296 (mttp) cc_final: 0.7951 (mttp) REVERT: C 70 LYS cc_start: 0.8259 (mttt) cc_final: 0.7995 (mttt) REVERT: C 157 ILE cc_start: 0.8467 (tp) cc_final: 0.8162 (tp) REVERT: C 161 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6531 (mpp) REVERT: C 192 ARG cc_start: 0.8516 (mtm180) cc_final: 0.8203 (mtm-85) REVERT: C 221 GLU cc_start: 0.7896 (tp30) cc_final: 0.7593 (tp30) REVERT: C 451 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7529 (mtt180) REVERT: C 469 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6863 (tp) REVERT: C 494 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7440 (mttp) REVERT: C 569 PHE cc_start: 0.7744 (t80) cc_final: 0.7456 (t80) REVERT: C 628 THR cc_start: 0.7811 (m) cc_final: 0.7561 (p) REVERT: C 643 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.6855 (p0) REVERT: C 668 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7751 (tm) REVERT: C 679 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8022 (ttmt) REVERT: C 683 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.5633 (p0) REVERT: C 690 ILE cc_start: 0.7024 (mt) cc_final: 0.6573 (mm) REVERT: C 693 VAL cc_start: 0.7949 (t) cc_final: 0.7299 (p) REVERT: C 777 ARG cc_start: 0.8232 (mmm160) cc_final: 0.8015 (mmp80) REVERT: C 793 LYS cc_start: 0.8070 (mttp) cc_final: 0.7774 (mttm) REVERT: C 802 CYS cc_start: 0.6862 (m) cc_final: 0.6153 (t) REVERT: C 915 GLU cc_start: 0.8673 (pp20) cc_final: 0.8128 (pp20) REVERT: E 222 ILE cc_start: 0.8213 (tp) cc_final: 0.7924 (tp) REVERT: E 418 LEU cc_start: 0.4823 (tp) cc_final: 0.4528 (tp) outliers start: 87 outliers final: 51 residues processed: 404 average time/residue: 0.2746 time to fit residues: 164.7537 Evaluate side-chains 405 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 348 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 654 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 757 ASP Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS C 299 ASN ** C 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15236 Z= 0.277 Angle : 0.710 10.868 20639 Z= 0.351 Chirality : 0.042 0.188 2512 Planarity : 0.004 0.052 2611 Dihedral : 4.700 24.004 2057 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.18 % Allowed : 25.76 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1914 helix: 0.83 (0.16), residues: 1089 sheet: -4.07 (0.97), residues: 10 loop : -1.85 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 137 HIS 0.008 0.001 HIS C 508 PHE 0.022 0.002 PHE A 402 TYR 0.031 0.002 TYR A 260 ARG 0.009 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 373 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.7459 (m-40) cc_final: 0.7251 (m-40) REVERT: A 102 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7325 (m-40) REVERT: A 113 GLU cc_start: 0.6556 (mp0) cc_final: 0.6118 (mp0) REVERT: A 117 LYS cc_start: 0.8683 (tttt) cc_final: 0.7963 (tptp) REVERT: A 185 LYS cc_start: 0.7253 (ttpp) cc_final: 0.6995 (mtpt) REVERT: A 235 GLN cc_start: 0.7009 (mp10) cc_final: 0.6602 (mp10) REVERT: A 281 GLU cc_start: 0.7517 (tp30) cc_final: 0.7140 (tp30) REVERT: A 315 LYS cc_start: 0.7575 (mmtm) cc_final: 0.7269 (mmtp) REVERT: A 331 ASP cc_start: 0.7196 (t0) cc_final: 0.6900 (t0) REVERT: A 338 LYS cc_start: 0.8615 (tptp) cc_final: 0.8172 (tptp) REVERT: A 386 ASN cc_start: 0.7993 (t0) cc_final: 0.7775 (t0) REVERT: A 451 VAL cc_start: 0.7829 (t) cc_final: 0.7618 (t) REVERT: A 627 ASP cc_start: 0.7488 (m-30) cc_final: 0.7176 (m-30) REVERT: A 705 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 712 GLN cc_start: 0.7084 (tm-30) cc_final: 0.6841 (tt0) REVERT: A 721 MET cc_start: 0.7773 (tpp) cc_final: 0.7567 (tpp) REVERT: A 761 TYR cc_start: 0.7315 (m-80) cc_final: 0.6837 (m-80) REVERT: C 15 MET cc_start: 0.7583 (tpp) cc_final: 0.7356 (tpp) REVERT: C 48 LYS cc_start: 0.8358 (mttp) cc_final: 0.8006 (mttp) REVERT: C 70 LYS cc_start: 0.8229 (mttt) cc_final: 0.7974 (mttt) REVERT: C 142 ILE cc_start: 0.8034 (mm) cc_final: 0.7769 (mt) REVERT: C 156 ASP cc_start: 0.8315 (m-30) cc_final: 0.8029 (m-30) REVERT: C 157 ILE cc_start: 0.8531 (tp) cc_final: 0.8207 (tp) REVERT: C 161 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6605 (mpp) REVERT: C 192 ARG cc_start: 0.8627 (mtm180) cc_final: 0.8329 (mtm-85) REVERT: C 221 GLU cc_start: 0.7915 (tp30) cc_final: 0.7618 (tp30) REVERT: C 451 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7548 (mtt180) REVERT: C 469 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6948 (tp) REVERT: C 494 LYS cc_start: 0.7695 (mtpt) cc_final: 0.7466 (mttp) REVERT: C 593 MET cc_start: 0.8073 (tpp) cc_final: 0.7576 (tpp) REVERT: C 634 LEU cc_start: 0.7636 (tt) cc_final: 0.7392 (tp) REVERT: C 679 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7971 (ttmt) REVERT: C 690 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6831 (mm) REVERT: C 693 VAL cc_start: 0.8084 (t) cc_final: 0.7453 (p) REVERT: C 706 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6516 (mmt) REVERT: C 802 CYS cc_start: 0.6981 (m) cc_final: 0.6304 (t) REVERT: D 7 GLN cc_start: 0.7018 (mp10) cc_final: 0.6719 (mp10) REVERT: E 154 ARG cc_start: 0.6585 (mtm110) cc_final: 0.6111 (mtm180) REVERT: E 222 ILE cc_start: 0.8254 (tp) cc_final: 0.7966 (tp) REVERT: E 418 LEU cc_start: 0.5107 (tp) cc_final: 0.4900 (tp) outliers start: 83 outliers final: 55 residues processed: 419 average time/residue: 0.2858 time to fit residues: 175.0783 Evaluate side-chains 419 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 359 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 757 ASP Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.0170 chunk 170 optimal weight: 0.7980 chunk 37 optimal weight: 0.0670 chunk 111 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 157 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS C 173 HIS C 299 ASN ** C 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15236 Z= 0.178 Angle : 0.681 13.166 20639 Z= 0.325 Chirality : 0.039 0.166 2512 Planarity : 0.004 0.053 2611 Dihedral : 4.353 22.656 2057 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.43 % Allowed : 28.51 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.20), residues: 1914 helix: 1.06 (0.16), residues: 1087 sheet: -3.88 (1.11), residues: 10 loop : -1.80 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 123 HIS 0.005 0.001 HIS C 173 PHE 0.024 0.001 PHE C 482 TYR 0.036 0.001 TYR A 260 ARG 0.009 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 365 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.7536 (m-40) cc_final: 0.7313 (m-40) REVERT: A 102 ASN cc_start: 0.7589 (t0) cc_final: 0.7282 (m-40) REVERT: A 104 LEU cc_start: 0.7138 (tp) cc_final: 0.6933 (tp) REVERT: A 117 LYS cc_start: 0.8576 (tttt) cc_final: 0.7815 (tptp) REVERT: A 139 TYR cc_start: 0.7355 (t80) cc_final: 0.7137 (t80) REVERT: A 235 GLN cc_start: 0.6987 (mp10) cc_final: 0.6624 (mp10) REVERT: A 315 LYS cc_start: 0.7534 (mmtm) cc_final: 0.7240 (mmtp) REVERT: A 324 ASN cc_start: 0.7998 (t0) cc_final: 0.7147 (p0) REVERT: A 331 ASP cc_start: 0.7126 (t0) cc_final: 0.6830 (t0) REVERT: A 338 LYS cc_start: 0.8526 (tptp) cc_final: 0.8076 (tptp) REVERT: A 419 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7508 (Cg_endo) REVERT: A 451 VAL cc_start: 0.7708 (t) cc_final: 0.7490 (t) REVERT: A 705 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7020 (mm-30) REVERT: A 721 MET cc_start: 0.7757 (tpp) cc_final: 0.7502 (tpp) REVERT: A 761 TYR cc_start: 0.7296 (m-80) cc_final: 0.6838 (m-80) REVERT: C 48 LYS cc_start: 0.8314 (mttp) cc_final: 0.7949 (mttp) REVERT: C 70 LYS cc_start: 0.8283 (mttt) cc_final: 0.7912 (mttt) REVERT: C 142 ILE cc_start: 0.7993 (mm) cc_final: 0.7736 (mt) REVERT: C 157 ILE cc_start: 0.8528 (tp) cc_final: 0.8220 (tp) REVERT: C 161 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6531 (mpp) REVERT: C 192 ARG cc_start: 0.8498 (mtm180) cc_final: 0.8162 (mtm-85) REVERT: C 221 GLU cc_start: 0.7891 (tp30) cc_final: 0.7559 (tp30) REVERT: C 469 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6782 (tp) REVERT: C 569 PHE cc_start: 0.7771 (t80) cc_final: 0.7347 (t80) REVERT: C 628 THR cc_start: 0.7967 (m) cc_final: 0.7627 (p) REVERT: C 634 LEU cc_start: 0.7591 (tt) cc_final: 0.7368 (tp) REVERT: C 643 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.6912 (p0) REVERT: C 683 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6421 (p0) REVERT: C 690 ILE cc_start: 0.7103 (mt) cc_final: 0.6720 (mm) REVERT: C 693 VAL cc_start: 0.7905 (t) cc_final: 0.7260 (p) REVERT: C 793 LYS cc_start: 0.8071 (mttp) cc_final: 0.7737 (mttm) REVERT: C 802 CYS cc_start: 0.6877 (m) cc_final: 0.6215 (t) REVERT: D 7 GLN cc_start: 0.6809 (mp10) cc_final: 0.6483 (mp10) REVERT: E 222 ILE cc_start: 0.8223 (tp) cc_final: 0.7917 (tp) REVERT: E 418 LEU cc_start: 0.5040 (tp) cc_final: 0.4825 (tp) outliers start: 71 outliers final: 51 residues processed: 402 average time/residue: 0.2623 time to fit residues: 155.3131 Evaluate side-chains 405 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 350 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 607 ASP Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 757 ASP Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS C 299 ASN ** C 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15236 Z= 0.209 Angle : 0.686 11.043 20639 Z= 0.331 Chirality : 0.039 0.166 2512 Planarity : 0.004 0.051 2611 Dihedral : 4.434 23.418 2057 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.62 % Allowed : 29.82 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1914 helix: 0.97 (0.16), residues: 1089 sheet: -0.61 (1.23), residues: 20 loop : -1.89 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 137 HIS 0.004 0.001 HIS C 508 PHE 0.015 0.001 PHE A 402 TYR 0.035 0.001 TYR A 260 ARG 0.009 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 364 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6089 (OUTLIER) cc_final: 0.5783 (tmt170) REVERT: A 98 ASN cc_start: 0.7571 (m-40) cc_final: 0.7352 (m-40) REVERT: A 102 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7295 (m-40) REVERT: A 104 LEU cc_start: 0.7068 (tp) cc_final: 0.6777 (tp) REVERT: A 117 LYS cc_start: 0.8601 (tttt) cc_final: 0.7845 (tptp) REVERT: A 139 TYR cc_start: 0.7382 (t80) cc_final: 0.7165 (t80) REVERT: A 146 ARG cc_start: 0.5261 (ttt-90) cc_final: 0.4926 (ttt-90) REVERT: A 229 LYS cc_start: 0.7128 (mtmm) cc_final: 0.6864 (mtmm) REVERT: A 235 GLN cc_start: 0.6966 (mp10) cc_final: 0.6638 (mp10) REVERT: A 251 PHE cc_start: 0.8158 (t80) cc_final: 0.7941 (t80) REVERT: A 315 LYS cc_start: 0.7504 (mmtm) cc_final: 0.7167 (mmtp) REVERT: A 331 ASP cc_start: 0.7180 (t0) cc_final: 0.6887 (t0) REVERT: A 451 VAL cc_start: 0.7787 (t) cc_final: 0.7575 (t) REVERT: A 705 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7130 (mm-30) REVERT: A 721 MET cc_start: 0.7784 (tpp) cc_final: 0.7555 (tpp) REVERT: A 761 TYR cc_start: 0.7320 (m-80) cc_final: 0.6875 (m-80) REVERT: C 48 LYS cc_start: 0.8341 (mttp) cc_final: 0.7776 (mttm) REVERT: C 142 ILE cc_start: 0.8016 (mm) cc_final: 0.7787 (mt) REVERT: C 156 ASP cc_start: 0.8269 (m-30) cc_final: 0.7938 (m-30) REVERT: C 157 ILE cc_start: 0.8533 (tp) cc_final: 0.8220 (tp) REVERT: C 161 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6530 (mpp) REVERT: C 192 ARG cc_start: 0.8555 (mtm180) cc_final: 0.8207 (mtm-85) REVERT: C 469 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6843 (tp) REVERT: C 494 LYS cc_start: 0.7695 (mtpt) cc_final: 0.7421 (mttp) REVERT: C 569 PHE cc_start: 0.7772 (t80) cc_final: 0.7374 (t80) REVERT: C 628 THR cc_start: 0.8013 (m) cc_final: 0.7668 (p) REVERT: C 634 LEU cc_start: 0.7645 (tt) cc_final: 0.7418 (tp) REVERT: C 643 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7571 (p0) REVERT: C 690 ILE cc_start: 0.7236 (mt) cc_final: 0.6845 (mm) REVERT: C 693 VAL cc_start: 0.7928 (t) cc_final: 0.7283 (p) REVERT: C 777 ARG cc_start: 0.8219 (mmm160) cc_final: 0.8013 (mmp80) REVERT: C 793 LYS cc_start: 0.8224 (mttp) cc_final: 0.7800 (mttp) REVERT: E 222 ILE cc_start: 0.8266 (tp) cc_final: 0.7988 (tp) REVERT: E 418 LEU cc_start: 0.5251 (tp) cc_final: 0.4968 (tp) outliers start: 74 outliers final: 55 residues processed: 408 average time/residue: 0.2761 time to fit residues: 163.2749 Evaluate side-chains 413 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 353 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 148 optimal weight: 0.0170 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS C 299 ASN C 663 GLN C 887 ASN D 65 HIS ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15236 Z= 0.177 Angle : 0.683 11.840 20639 Z= 0.328 Chirality : 0.039 0.171 2512 Planarity : 0.004 0.052 2611 Dihedral : 4.282 22.467 2057 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.93 % Allowed : 30.26 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1914 helix: 1.06 (0.16), residues: 1082 sheet: -0.58 (1.24), residues: 20 loop : -1.84 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 123 HIS 0.004 0.001 HIS C 173 PHE 0.025 0.001 PHE C 482 TYR 0.026 0.001 TYR A 260 ARG 0.009 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 360 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6021 (OUTLIER) cc_final: 0.5746 (tmt170) REVERT: A 98 ASN cc_start: 0.7569 (m-40) cc_final: 0.7351 (m-40) REVERT: A 102 ASN cc_start: 0.7576 (t0) cc_final: 0.7279 (m-40) REVERT: A 104 LEU cc_start: 0.7020 (tp) cc_final: 0.6675 (tp) REVERT: A 117 LYS cc_start: 0.8567 (tttt) cc_final: 0.7827 (tptp) REVERT: A 146 ARG cc_start: 0.5316 (ttt-90) cc_final: 0.4964 (ttt-90) REVERT: A 229 LYS cc_start: 0.7046 (mtmm) cc_final: 0.6751 (mtmm) REVERT: A 235 GLN cc_start: 0.6901 (mp10) cc_final: 0.6622 (mp10) REVERT: A 242 ARG cc_start: 0.7488 (ptt90) cc_final: 0.6812 (ptt90) REVERT: A 286 GLU cc_start: 0.7536 (mp0) cc_final: 0.6910 (mp0) REVERT: A 290 LYS cc_start: 0.8475 (ptmt) cc_final: 0.8220 (ptmt) REVERT: A 315 LYS cc_start: 0.7543 (mmtm) cc_final: 0.7205 (mmtp) REVERT: A 331 ASP cc_start: 0.7244 (t0) cc_final: 0.6941 (t0) REVERT: A 338 LYS cc_start: 0.8820 (tptp) cc_final: 0.8559 (tptp) REVERT: A 419 PRO cc_start: 0.7711 (Cg_exo) cc_final: 0.7443 (Cg_endo) REVERT: A 450 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.7015 (mmm) REVERT: A 451 VAL cc_start: 0.7711 (t) cc_final: 0.7492 (t) REVERT: A 705 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 721 MET cc_start: 0.7771 (tpp) cc_final: 0.7511 (tpp) REVERT: A 761 TYR cc_start: 0.7314 (m-80) cc_final: 0.6837 (m-80) REVERT: C 48 LYS cc_start: 0.8347 (mttp) cc_final: 0.7940 (mttp) REVERT: C 70 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8097 (mttt) REVERT: C 142 ILE cc_start: 0.8005 (mm) cc_final: 0.7749 (mt) REVERT: C 157 ILE cc_start: 0.8541 (tp) cc_final: 0.8226 (tp) REVERT: C 161 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6485 (mpp) REVERT: C 192 ARG cc_start: 0.8480 (mtm180) cc_final: 0.8137 (mtm-85) REVERT: C 272 ARG cc_start: 0.7495 (ttt90) cc_final: 0.7145 (ttt90) REVERT: C 593 MET cc_start: 0.8066 (tpp) cc_final: 0.7632 (tpp) REVERT: C 628 THR cc_start: 0.7856 (m) cc_final: 0.7568 (p) REVERT: C 634 LEU cc_start: 0.7586 (tt) cc_final: 0.7369 (tp) REVERT: C 643 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.6857 (p0) REVERT: C 683 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.5911 (p0) REVERT: C 690 ILE cc_start: 0.7236 (mt) cc_final: 0.6839 (mm) REVERT: C 693 VAL cc_start: 0.7912 (t) cc_final: 0.7255 (p) REVERT: C 777 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7999 (mmp80) REVERT: C 793 LYS cc_start: 0.8200 (mttp) cc_final: 0.7744 (mttm) REVERT: C 802 CYS cc_start: 0.6896 (m) cc_final: 0.6303 (t) REVERT: E 222 ILE cc_start: 0.8231 (tp) cc_final: 0.7946 (tp) REVERT: E 418 LEU cc_start: 0.5268 (tp) cc_final: 0.4980 (tp) outliers start: 63 outliers final: 48 residues processed: 393 average time/residue: 0.2921 time to fit residues: 167.9323 Evaluate side-chains 407 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 354 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.8980 chunk 180 optimal weight: 0.0040 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 15236 Z= 0.224 Angle : 0.702 11.817 20639 Z= 0.342 Chirality : 0.040 0.167 2512 Planarity : 0.004 0.056 2611 Dihedral : 4.430 22.965 2057 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.37 % Allowed : 30.38 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1914 helix: 0.93 (0.16), residues: 1091 sheet: -0.53 (1.22), residues: 20 loop : -1.84 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 137 HIS 0.004 0.001 HIS D 64 PHE 0.026 0.001 PHE A 251 TYR 0.048 0.001 TYR A 260 ARG 0.010 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 357 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5874 (tmt170) REVERT: A 98 ASN cc_start: 0.7572 (m-40) cc_final: 0.7367 (m-40) REVERT: A 102 ASN cc_start: 0.7588 (t0) cc_final: 0.7302 (m-40) REVERT: A 104 LEU cc_start: 0.6937 (tp) cc_final: 0.6635 (tp) REVERT: A 117 LYS cc_start: 0.8598 (tttt) cc_final: 0.7810 (tptp) REVERT: A 146 ARG cc_start: 0.5310 (ttt-90) cc_final: 0.4988 (ttt-90) REVERT: A 229 LYS cc_start: 0.7037 (mtmm) cc_final: 0.6689 (mtmm) REVERT: A 235 GLN cc_start: 0.6982 (mp10) cc_final: 0.6666 (mp10) REVERT: A 242 ARG cc_start: 0.7650 (ptt90) cc_final: 0.6941 (ptt90) REVERT: A 290 LYS cc_start: 0.8483 (ptmt) cc_final: 0.8181 (ptmt) REVERT: A 315 LYS cc_start: 0.7495 (mmtm) cc_final: 0.7175 (mmtp) REVERT: A 324 ASN cc_start: 0.8046 (t0) cc_final: 0.7185 (p0) REVERT: A 331 ASP cc_start: 0.7263 (t0) cc_final: 0.6948 (t0) REVERT: A 419 PRO cc_start: 0.7765 (Cg_exo) cc_final: 0.7513 (Cg_endo) REVERT: A 451 VAL cc_start: 0.7788 (t) cc_final: 0.7573 (t) REVERT: A 705 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7122 (mm-30) REVERT: A 712 GLN cc_start: 0.7004 (tm-30) cc_final: 0.6716 (tt0) REVERT: A 719 MET cc_start: 0.5432 (mtt) cc_final: 0.5188 (mtp) REVERT: A 721 MET cc_start: 0.7830 (tpp) cc_final: 0.7588 (tpp) REVERT: A 761 TYR cc_start: 0.7358 (m-80) cc_final: 0.6926 (m-80) REVERT: C 48 LYS cc_start: 0.8375 (mttp) cc_final: 0.7949 (mttp) REVERT: C 70 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8192 (mttt) REVERT: C 142 ILE cc_start: 0.8058 (mm) cc_final: 0.7822 (mt) REVERT: C 156 ASP cc_start: 0.8299 (m-30) cc_final: 0.7998 (m-30) REVERT: C 157 ILE cc_start: 0.8548 (tp) cc_final: 0.8235 (tp) REVERT: C 161 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6513 (mpp) REVERT: C 170 VAL cc_start: 0.7322 (OUTLIER) cc_final: 0.7084 (m) REVERT: C 192 ARG cc_start: 0.8564 (mtm180) cc_final: 0.8216 (mtm-85) REVERT: C 569 PHE cc_start: 0.7805 (t80) cc_final: 0.7422 (t80) REVERT: C 593 MET cc_start: 0.8094 (tpp) cc_final: 0.7664 (tpp) REVERT: C 628 THR cc_start: 0.8019 (m) cc_final: 0.7739 (p) REVERT: C 634 LEU cc_start: 0.7673 (tt) cc_final: 0.7428 (tp) REVERT: C 664 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6342 (mpt-90) REVERT: C 690 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6946 (mm) REVERT: C 693 VAL cc_start: 0.7934 (t) cc_final: 0.7297 (p) REVERT: C 793 LYS cc_start: 0.8226 (mttp) cc_final: 0.7816 (mttm) REVERT: E 138 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6804 (mm-40) REVERT: E 222 ILE cc_start: 0.8254 (tp) cc_final: 0.7970 (tp) REVERT: E 418 LEU cc_start: 0.5587 (tp) cc_final: 0.5312 (tp) outliers start: 70 outliers final: 55 residues processed: 395 average time/residue: 0.2842 time to fit residues: 162.7831 Evaluate side-chains 408 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 347 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 113 optimal weight: 0.0030 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 155 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 overall best weight: 0.3668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 700 HIS C 173 HIS C 680 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15236 Z= 0.190 Angle : 0.702 12.196 20639 Z= 0.340 Chirality : 0.039 0.179 2512 Planarity : 0.004 0.072 2611 Dihedral : 4.356 22.753 2057 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.30 % Allowed : 30.19 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1914 helix: 1.02 (0.16), residues: 1081 sheet: -0.40 (1.26), residues: 20 loop : -1.75 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 123 HIS 0.004 0.001 HIS C 173 PHE 0.025 0.001 PHE C 482 TYR 0.039 0.001 TYR A 260 ARG 0.009 0.000 ARG C 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 358 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5800 (tmt170) REVERT: A 98 ASN cc_start: 0.7575 (m-40) cc_final: 0.7369 (m-40) REVERT: A 102 ASN cc_start: 0.7579 (t0) cc_final: 0.7296 (m-40) REVERT: A 104 LEU cc_start: 0.6962 (tp) cc_final: 0.6751 (tp) REVERT: A 117 LYS cc_start: 0.8583 (tttt) cc_final: 0.7799 (tptp) REVERT: A 146 ARG cc_start: 0.5289 (ttt-90) cc_final: 0.4963 (ttt-90) REVERT: A 229 LYS cc_start: 0.6991 (mtmm) cc_final: 0.6669 (mtmm) REVERT: A 235 GLN cc_start: 0.6873 (mp10) cc_final: 0.6646 (mp10) REVERT: A 242 ARG cc_start: 0.7580 (ptt90) cc_final: 0.6948 (ptt90) REVERT: A 290 LYS cc_start: 0.8413 (ptmt) cc_final: 0.8122 (ptmt) REVERT: A 315 LYS cc_start: 0.7441 (mmtm) cc_final: 0.7115 (mmtp) REVERT: A 324 ASN cc_start: 0.8016 (t0) cc_final: 0.7157 (p0) REVERT: A 331 ASP cc_start: 0.7243 (t0) cc_final: 0.6890 (t0) REVERT: A 338 LYS cc_start: 0.8758 (tptp) cc_final: 0.8475 (tptp) REVERT: A 419 PRO cc_start: 0.7729 (Cg_exo) cc_final: 0.7478 (Cg_endo) REVERT: A 450 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.7000 (mmm) REVERT: A 451 VAL cc_start: 0.7751 (t) cc_final: 0.7522 (t) REVERT: A 606 PHE cc_start: 0.4729 (m-10) cc_final: 0.4160 (m-10) REVERT: A 705 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7123 (mm-30) REVERT: A 712 GLN cc_start: 0.6958 (tm-30) cc_final: 0.6705 (tt0) REVERT: A 719 MET cc_start: 0.5484 (mtt) cc_final: 0.5260 (mtp) REVERT: A 721 MET cc_start: 0.7791 (tpp) cc_final: 0.7503 (tpp) REVERT: A 761 TYR cc_start: 0.7360 (m-80) cc_final: 0.6946 (m-80) REVERT: C 48 LYS cc_start: 0.8368 (mttp) cc_final: 0.7929 (mttp) REVERT: C 70 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8158 (mttt) REVERT: C 157 ILE cc_start: 0.8546 (tp) cc_final: 0.8228 (tp) REVERT: C 161 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6491 (mpp) REVERT: C 192 ARG cc_start: 0.8472 (mtm180) cc_final: 0.8127 (mtm-85) REVERT: C 272 ARG cc_start: 0.7762 (ttt90) cc_final: 0.7468 (ttt90) REVERT: C 569 PHE cc_start: 0.7772 (t80) cc_final: 0.7388 (t80) REVERT: C 593 MET cc_start: 0.8072 (tpp) cc_final: 0.7685 (tpp) REVERT: C 628 THR cc_start: 0.7996 (m) cc_final: 0.7737 (p) REVERT: C 634 LEU cc_start: 0.7648 (tt) cc_final: 0.7418 (tp) REVERT: C 643 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.6683 (p0) REVERT: C 664 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6420 (mpt-90) REVERT: C 683 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.5984 (p0) REVERT: C 690 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6893 (mm) REVERT: C 693 VAL cc_start: 0.7938 (t) cc_final: 0.7293 (p) REVERT: C 793 LYS cc_start: 0.8206 (mttp) cc_final: 0.7788 (mttm) REVERT: E 138 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6745 (mm-40) REVERT: E 222 ILE cc_start: 0.8235 (tp) cc_final: 0.7953 (tp) REVERT: E 418 LEU cc_start: 0.5467 (tp) cc_final: 0.5187 (tp) outliers start: 69 outliers final: 52 residues processed: 394 average time/residue: 0.2843 time to fit residues: 162.3643 Evaluate side-chains 418 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 358 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 47 optimal weight: 0.0070 chunk 143 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 chunk 155 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 0.0020 chunk 28 optimal weight: 0.7980 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 677 ASN A 700 HIS C 680 ASN ** E 236 ASN ** 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 = 0.4184 r_free = 0.4184 target = 0.154742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.131069 restraints weight = 30604.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135227 restraints weight = 17158.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138059 restraints weight = 10889.243| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15236 Z= 0.180 Angle : 0.704 12.293 20639 Z= 0.338 Chirality : 0.039 0.184 2512 Planarity : 0.004 0.076 2611 Dihedral : 4.245 21.931 2057 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.62 % Allowed : 30.75 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1914 helix: 1.08 (0.16), residues: 1085 sheet: -0.08 (1.20), residues: 20 loop : -1.76 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 123 HIS 0.003 0.001 HIS C 173 PHE 0.018 0.001 PHE A 251 TYR 0.029 0.001 TYR A 260 ARG 0.009 0.000 ARG C 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.56 seconds wall clock time: 70 minutes 8.11 seconds (4208.11 seconds total)