Starting phenix.real_space_refine on Fri Jan 16 15:56:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m2w_23635/01_2026/7m2w_23635.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m2w_23635/01_2026/7m2w_23635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m2w_23635/01_2026/7m2w_23635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m2w_23635/01_2026/7m2w_23635.map" model { file = "/net/cci-nas-00/data/ceres_data/7m2w_23635/01_2026/7m2w_23635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m2w_23635/01_2026/7m2w_23635.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.632 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 168 5.16 5 C 25005 2.51 5 N 6618 2.21 5 O 7563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 297 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39366 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3450 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3547 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 20, 'TRANS': 432} Chain: "C" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3481 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 424} Chain breaks: 1 Chain: "D" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3500 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 20, 'TRANS': 426} Chain breaks: 1 Chain: "E" Number of atoms: 5899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5899 Classifications: {'peptide': 707} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 681} Chain breaks: 5 Chain: "F" Number of atoms: 5569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5569 Classifications: {'peptide': 674} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 654} Chain breaks: 1 Chain: "G" Number of atoms: 5935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5935 Classifications: {'peptide': 712} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 685} Chain breaks: 5 Chain: "H" Number of atoms: 5569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5569 Classifications: {'peptide': 674} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 654} Chain breaks: 1 Chain: "U" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 352 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 792 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 352 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Y" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 792 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.52, per 1000 atoms: 0.22 Number of scatterers: 39366 At special positions: 0 Unit cell: (220.272, 165.204, 211.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 12 15.00 O 7563 8.00 N 6618 7.00 C 25005 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9278 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 23 sheets defined 63.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 72 through 83 removed outlier: 4.489A pdb=" N ILE B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 104 through 115 removed outlier: 3.613A pdb=" N GLY B 108 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 179 through 198 removed outlier: 4.903A pdb=" N TYR B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.534A pdb=" N THR B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.717A pdb=" N ILE B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 327 through 342 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.660A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.666A pdb=" N TYR B 407 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 441 removed outlier: 3.610A pdb=" N GLU B 441 " --> pdb=" O TYR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'A' and resid 11 through 29 Processing helix chain 'A' and resid 72 through 83 removed outlier: 4.535A pdb=" N ILE A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.520A pdb=" N GLY A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.772A pdb=" N SER A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.641A pdb=" N GLY A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 197 removed outlier: 4.086A pdb=" N ARG A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 227 through 244 removed outlier: 4.229A pdb=" N ILE A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 384 through 398 removed outlier: 4.209A pdb=" N ASN A 389 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 415 through 441 removed outlier: 3.676A pdb=" N VAL A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 441 " --> pdb=" O TYR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 removed outlier: 3.803A pdb=" N ASP A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 29 Processing helix chain 'C' and resid 72 through 83 removed outlier: 4.523A pdb=" N ILE C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.536A pdb=" N GLY C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 129 Processing helix chain 'C' and resid 144 through 159 Processing helix chain 'C' and resid 179 through 197 removed outlier: 3.992A pdb=" N ARG C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.886A pdb=" N GLN C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 327 through 342 Processing helix chain 'C' and resid 384 through 398 removed outlier: 4.612A pdb=" N ASN C 389 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 440 Processing helix chain 'C' and resid 442 through 445 Processing helix chain 'C' and resid 446 through 451 Processing helix chain 'D' and resid 11 through 28 Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 104 through 115 removed outlier: 3.689A pdb=" N GLY D 108 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 3.568A pdb=" N SER D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 removed outlier: 4.292A pdb=" N ASP D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 197 removed outlier: 4.061A pdb=" N ARG D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 223 through 226 Processing helix chain 'D' and resid 227 through 244 removed outlier: 4.878A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 290 through 298 Processing helix chain 'D' and resid 327 through 340 removed outlier: 4.095A pdb=" N GLN D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 Processing helix chain 'D' and resid 384 through 399 removed outlier: 3.770A pdb=" N ASN D 389 " --> pdb=" O ASN D 385 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS D 396 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 441 removed outlier: 3.950A pdb=" N GLU D 441 " --> pdb=" O TYR D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 445 Processing helix chain 'D' and resid 446 through 451 removed outlier: 3.535A pdb=" N VAL D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 3.752A pdb=" N LYS E 45 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 67 Processing helix chain 'E' and resid 99 through 127 removed outlier: 4.065A pdb=" N TYR E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 131 through 149 removed outlier: 4.087A pdb=" N LEU E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 157 through 165 Processing helix chain 'E' and resid 169 through 180 removed outlier: 3.543A pdb=" N THR E 180 " --> pdb=" O ILE E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 206 Processing helix chain 'E' and resid 222 through 226 removed outlier: 3.626A pdb=" N SER E 225 " --> pdb=" O ASN E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.747A pdb=" N ILE E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 276 Processing helix chain 'E' and resid 276 through 290 Processing helix chain 'E' and resid 337 through 361 Processing helix chain 'E' and resid 380 through 387 removed outlier: 4.532A pdb=" N GLY E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 412 Processing helix chain 'E' and resid 414 through 427 Processing helix chain 'E' and resid 431 through 452 removed outlier: 5.887A pdb=" N GLY E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 471 removed outlier: 3.501A pdb=" N LEU E 462 " --> pdb=" O TYR E 458 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 471 " --> pdb=" O LEU E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 481 Processing helix chain 'E' and resid 490 through 496 Processing helix chain 'E' and resid 569 through 573 removed outlier: 3.551A pdb=" N ILE E 572 " --> pdb=" O PRO E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 609 Processing helix chain 'E' and resid 609 through 614 removed outlier: 3.817A pdb=" N LYS E 613 " --> pdb=" O THR E 609 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR E 614 " --> pdb=" O PRO E 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 609 through 614' Processing helix chain 'E' and resid 616 through 619 removed outlier: 3.785A pdb=" N HIS E 619 " --> pdb=" O GLY E 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 616 through 619' Processing helix chain 'E' and resid 620 through 625 Processing helix chain 'E' and resid 625 through 651 Processing helix chain 'E' and resid 651 through 663 Processing helix chain 'E' and resid 668 through 685 Processing helix chain 'E' and resid 692 through 717 removed outlier: 4.173A pdb=" N ALA E 715 " --> pdb=" O LYS E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 726 removed outlier: 3.866A pdb=" N ASP E 721 " --> pdb=" O CYS E 718 " (cutoff:3.500A) Proline residue: E 722 - end of helix removed outlier: 3.505A pdb=" N TYR E 725 " --> pdb=" O PRO E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 754 through 788 removed outlier: 3.758A pdb=" N LEU E 758 " --> pdb=" O GLU E 754 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR E 788 " --> pdb=" O GLN E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 802 through 812 Processing helix chain 'F' and resid 166 through 172 Processing helix chain 'F' and resid 173 through 176 removed outlier: 4.131A pdb=" N VAL F 176 " --> pdb=" O PRO F 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 173 through 176' Processing helix chain 'F' and resid 180 through 192 removed outlier: 4.116A pdb=" N TYR F 190 " --> pdb=" O LYS F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 242 removed outlier: 4.485A pdb=" N ALA F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY F 228 " --> pdb=" O ILE F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 275 removed outlier: 3.731A pdb=" N GLY F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 287 Processing helix chain 'F' and resid 287 through 301 Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.726A pdb=" N LEU F 307 " --> pdb=" O LEU F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 320 Processing helix chain 'F' and resid 324 through 353 Processing helix chain 'F' and resid 395 through 415 Processing helix chain 'F' and resid 418 through 435 Processing helix chain 'F' and resid 436 through 440 Processing helix chain 'F' and resid 442 through 467 removed outlier: 3.504A pdb=" N PHE F 446 " --> pdb=" O SER F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 481 Processing helix chain 'F' and resid 485 through 501 removed outlier: 3.619A pdb=" N MET F 489 " --> pdb=" O LYS F 485 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP F 498 " --> pdb=" O GLU F 494 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 499 " --> pdb=" O LYS F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 522 Processing helix chain 'F' and resid 525 through 530 Processing helix chain 'F' and resid 534 through 540 removed outlier: 4.003A pdb=" N ILE F 538 " --> pdb=" O ASN F 534 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 540 " --> pdb=" O SER F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 571 Processing helix chain 'F' and resid 581 through 616 removed outlier: 3.735A pdb=" N PHE F 593 " --> pdb=" O PHE F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 656 Processing helix chain 'F' and resid 656 through 669 Processing helix chain 'F' and resid 720 through 737 Processing helix chain 'F' and resid 757 through 793 Processing helix chain 'F' and resid 799 through 832 removed outlier: 3.788A pdb=" N GLY F 803 " --> pdb=" O ASN F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 845 Processing helix chain 'G' and resid 42 through 47 removed outlier: 3.520A pdb=" N SER G 47 " --> pdb=" O GLU G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 67 Processing helix chain 'G' and resid 99 through 127 removed outlier: 3.899A pdb=" N TYR G 112 " --> pdb=" O ARG G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 149 removed outlier: 4.261A pdb=" N LEU G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 165 removed outlier: 4.865A pdb=" N ARG G 160 " --> pdb=" O GLU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 180 Processing helix chain 'G' and resid 181 through 206 Processing helix chain 'G' and resid 223 through 228 Processing helix chain 'G' and resid 244 through 258 removed outlier: 3.942A pdb=" N ILE G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 276 Processing helix chain 'G' and resid 276 through 289 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 337 through 361 removed outlier: 3.512A pdb=" N LEU G 361 " --> pdb=" O VAL G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 385 Processing helix chain 'G' and resid 388 through 413 Processing helix chain 'G' and resid 414 through 426 Processing helix chain 'G' and resid 431 through 442 Processing helix chain 'G' and resid 444 through 448 removed outlier: 3.592A pdb=" N THR G 447 " --> pdb=" O GLY G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.687A pdb=" N LEU G 462 " --> pdb=" O TYR G 458 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER G 471 " --> pdb=" O LEU G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 482 Processing helix chain 'G' and resid 490 through 496 Processing helix chain 'G' and resid 555 through 558 Processing helix chain 'G' and resid 575 through 609 Processing helix chain 'G' and resid 609 through 614 Processing helix chain 'G' and resid 616 through 619 Processing helix chain 'G' and resid 620 through 651 removed outlier: 4.982A pdb=" N ALA G 628 " --> pdb=" O ARG G 624 " (cutoff:3.500A) Processing helix chain 'G' and resid 651 through 663 Processing helix chain 'G' and resid 668 through 685 Processing helix chain 'G' and resid 686 through 691 Processing helix chain 'G' and resid 692 through 717 removed outlier: 4.213A pdb=" N ALA G 715 " --> pdb=" O LYS G 711 " (cutoff:3.500A) Processing helix chain 'G' and resid 721 through 725 Processing helix chain 'G' and resid 754 through 789 removed outlier: 3.526A pdb=" N LEU G 758 " --> pdb=" O GLU G 754 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU G 789 " --> pdb=" O GLU G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 812 Processing helix chain 'H' and resid 166 through 172 Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 180 through 192 removed outlier: 4.258A pdb=" N TYR H 190 " --> pdb=" O LYS H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 242 removed outlier: 4.703A pdb=" N ALA H 227 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY H 228 " --> pdb=" O ILE H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 275 removed outlier: 3.760A pdb=" N GLY H 275 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 287 Processing helix chain 'H' and resid 287 through 301 removed outlier: 3.882A pdb=" N THR H 301 " --> pdb=" O TYR H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 307 removed outlier: 3.737A pdb=" N LEU H 307 " --> pdb=" O LEU H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 320 Processing helix chain 'H' and resid 324 through 353 Processing helix chain 'H' and resid 387 through 390 removed outlier: 3.581A pdb=" N VAL H 390 " --> pdb=" O GLN H 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 387 through 390' Processing helix chain 'H' and resid 395 through 415 Processing helix chain 'H' and resid 418 through 435 Processing helix chain 'H' and resid 442 through 469 removed outlier: 3.515A pdb=" N PHE H 446 " --> pdb=" O SER H 442 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 479 Processing helix chain 'H' and resid 485 through 496 removed outlier: 3.907A pdb=" N MET H 489 " --> pdb=" O LYS H 485 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 510 through 522 removed outlier: 4.063A pdb=" N ARG H 514 " --> pdb=" O TYR H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 525 through 530 Processing helix chain 'H' and resid 534 through 539 removed outlier: 3.691A pdb=" N ILE H 538 " --> pdb=" O ASN H 534 " (cutoff:3.500A) Processing helix chain 'H' and resid 553 through 557 Processing helix chain 'H' and resid 567 through 572 removed outlier: 3.689A pdb=" N VAL H 571 " --> pdb=" O PRO H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 613 removed outlier: 3.966A pdb=" N PHE H 593 " --> pdb=" O PHE H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 621 through 656 removed outlier: 4.269A pdb=" N ARG H 625 " --> pdb=" O ASN H 621 " (cutoff:3.500A) Processing helix chain 'H' and resid 656 through 669 Processing helix chain 'H' and resid 720 through 738 Processing helix chain 'H' and resid 757 through 793 Processing helix chain 'H' and resid 800 through 832 removed outlier: 4.137A pdb=" N LYS H 804 " --> pdb=" O GLY H 800 " (cutoff:3.500A) Processing helix chain 'H' and resid 835 through 846 Processing helix chain 'U' and resid 165 through 204 Processing helix chain 'K' and resid 119 through 142 Processing helix chain 'K' and resid 157 through 161 removed outlier: 3.930A pdb=" N TYR K 161 " --> pdb=" O LYS K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 205 removed outlier: 3.611A pdb=" N GLU K 171 " --> pdb=" O SER K 167 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU K 203 " --> pdb=" O ARG K 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 205 removed outlier: 4.497A pdb=" N ALA X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU X 203 " --> pdb=" O ARG X 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 142 Processing helix chain 'Y' and resid 157 through 161 removed outlier: 3.892A pdb=" N TYR Y 161 " --> pdb=" O LYS Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 167 through 204 removed outlier: 4.175A pdb=" N GLU Y 171 " --> pdb=" O SER Y 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 93 removed outlier: 8.378A pdb=" N TRP B 93 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET B 68 " --> pdb=" O TRP B 93 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE B 67 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR B 7 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N MET B 69 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 9 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU B 4 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN B 137 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 6 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU B 139 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 8 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N SER B 141 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA B 10 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU B 134 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR B 168 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE B 136 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR B 170 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 138 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B 172 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N HIS B 140 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 200 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR B 201 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N PHE B 272 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 13.101A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE B 267 " --> pdb=" O MET B 380 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N MET B 380 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 374 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 317 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS B 353 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 318 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASN B 355 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN B 320 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY B 357 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 322 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.500A pdb=" N TRP A 93 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET A 68 " --> pdb=" O TRP A 93 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE A 67 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR A 7 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET A 69 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN A 9 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 10 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE A 136 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N TYR A 170 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 138 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A 172 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 167 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL A 202 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR A 169 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 204 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER A 171 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 201 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 357 removed outlier: 3.558A pdb=" N ASN A 317 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 66 through 69 removed outlier: 8.465A pdb=" N ILE C 67 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR C 7 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N MET C 69 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN C 9 " --> pdb=" O MET C 69 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU C 4 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER C 141 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS C 140 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 172 " --> pdb=" O HIS C 140 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASP C 205 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N PHE C 272 " --> pdb=" O ASP C 205 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE C 267 " --> pdb=" O MET C 380 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N MET C 380 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 317 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N HIS C 353 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C 318 " --> pdb=" O HIS C 353 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASN C 355 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN C 320 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 357 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE C 322 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 66 through 69 removed outlier: 8.306A pdb=" N ILE D 67 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR D 7 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N MET D 69 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN D 9 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU D 4 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE D 136 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE D 6 " --> pdb=" O PHE D 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 54 through 57 removed outlier: 3.758A pdb=" N LYS D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.732A pdb=" N LEU D 138 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL D 172 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 353 through 357 removed outlier: 8.453A pdb=" N HIS D 353 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 318 " --> pdb=" O HIS D 353 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN D 355 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN D 320 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY D 357 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE D 322 " --> pdb=" O GLY D 357 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 317 " --> pdb=" O ASN D 379 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AB4, first strand: chain 'E' and resid 301 through 302 removed outlier: 4.375A pdb=" N HIS Y 147 " --> pdb=" O VAL E 232 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 482 through 486 Processing sheet with id=AB6, first strand: chain 'F' and resid 364 through 366 Processing sheet with id=AB7, first strand: chain 'F' and resid 541 through 545 removed outlier: 3.670A pdb=" N ASP F 542 " --> pdb=" O ASP F 561 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 681 through 683 Processing sheet with id=AB9, first strand: chain 'G' and resid 75 through 77 Processing sheet with id=AC1, first strand: chain 'G' and resid 301 through 303 removed outlier: 3.592A pdb=" N THR K 149 " --> pdb=" O PHE G 234 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 483 through 486 Processing sheet with id=AC3, first strand: chain 'H' and resid 364 through 366 Processing sheet with id=AC4, first strand: chain 'H' and resid 541 through 545 Processing sheet with id=AC5, first strand: chain 'H' and resid 681 through 683 2274 hydrogen bonds defined for protein. 6699 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: 8.67 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6686 1.32 - 1.44: 10619 1.44 - 1.57: 22540 1.57 - 1.69: 20 1.69 - 1.82: 290 Bond restraints: 40155 Sorted by residual: bond pdb=" C HIS D 289 " pdb=" O HIS D 289 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.02e-02 9.61e+03 1.92e+01 bond pdb=" CA HIS D 289 " pdb=" C HIS D 289 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N HIS D 289 " pdb=" CA HIS D 289 " ideal model delta sigma weight residual 1.459 1.417 0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" CG LEU K 200 " pdb=" CD2 LEU K 200 " ideal model delta sigma weight residual 1.521 1.404 0.117 3.30e-02 9.18e+02 1.26e+01 bond pdb=" CZ ARG X 176 " pdb=" NH2 ARG X 176 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.24e+01 ... (remaining 40150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 53754 2.78 - 5.56: 557 5.56 - 8.34: 26 8.34 - 11.11: 1 11.11 - 13.89: 1 Bond angle restraints: 54339 Sorted by residual: angle pdb=" N CYS B 58 " pdb=" CA CYS B 58 " pdb=" C CYS B 58 " ideal model delta sigma weight residual 111.33 118.32 -6.99 1.21e+00 6.83e-01 3.34e+01 angle pdb=" OE1 GLN Y 122 " pdb=" CD GLN Y 122 " pdb=" NE2 GLN Y 122 " ideal model delta sigma weight residual 122.60 118.03 4.57 1.00e+00 1.00e+00 2.09e+01 angle pdb=" CB HIS K 147 " pdb=" CG HIS K 147 " pdb=" CD2 HIS K 147 " ideal model delta sigma weight residual 131.20 125.38 5.82 1.30e+00 5.92e-01 2.01e+01 angle pdb=" C GLY Y 144 " pdb=" N LYS Y 145 " pdb=" CA LYS Y 145 " ideal model delta sigma weight residual 120.63 127.80 -7.17 1.61e+00 3.86e-01 1.99e+01 angle pdb=" N CYS D 288 " pdb=" CA CYS D 288 " pdb=" C CYS D 288 " ideal model delta sigma weight residual 110.80 119.77 -8.97 2.13e+00 2.20e-01 1.77e+01 ... (remaining 54334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 23965 35.68 - 71.36: 365 71.36 - 107.05: 29 107.05 - 142.73: 1 142.73 - 178.41: 7 Dihedral angle restraints: 24367 sinusoidal: 10065 harmonic: 14302 Sorted by residual: dihedral pdb=" C5' GTP D 501 " pdb=" O5' GTP D 501 " pdb=" PA GTP D 501 " pdb=" O3A GTP D 501 " ideal model delta sinusoidal sigma weight residual 69.27 -112.32 -178.41 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.09 -169.64 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -99.57 168.84 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5217 0.061 - 0.123: 779 0.123 - 0.184: 47 0.184 - 0.245: 6 0.245 - 0.307: 3 Chirality restraints: 6052 Sorted by residual: chirality pdb=" CA GLU U 164 " pdb=" N GLU U 164 " pdb=" C GLU U 164 " pdb=" CB GLU U 164 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA CYS D 288 " pdb=" N CYS D 288 " pdb=" C CYS D 288 " pdb=" CB CYS D 288 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA GLU X 164 " pdb=" N GLU X 164 " pdb=" C GLU X 164 " pdb=" CB GLU X 164 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 6049 not shown) Planarity restraints: 6995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Y 186 " 0.112 2.00e-02 2.50e+03 6.76e-02 9.14e+01 pdb=" CG TYR Y 186 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR Y 186 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR Y 186 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR Y 186 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR Y 186 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR Y 186 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR Y 186 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Y 134 " -0.064 2.00e-02 2.50e+03 4.02e-02 2.83e+01 pdb=" CG PHE Y 134 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE Y 134 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE Y 134 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE Y 134 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE Y 134 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE Y 134 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 186 " -0.048 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR K 186 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR K 186 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR K 186 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR K 186 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR K 186 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR K 186 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR K 186 " -0.046 2.00e-02 2.50e+03 ... (remaining 6992 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 4 2.04 - 2.75: 5686 2.75 - 3.47: 58288 3.47 - 4.18: 96278 4.18 - 4.90: 174123 Nonbonded interactions: 334379 Sorted by model distance: nonbonded pdb=" NE ARG C 59 " pdb=" SG CYS D 288 " model vdw 1.321 3.480 nonbonded pdb=" NH2 ARG E 14 " pdb=" NE2 HIS Y 170 " model vdw 1.498 3.200 nonbonded pdb=" CD ARG C 59 " pdb=" SG CYS D 288 " model vdw 2.004 3.800 nonbonded pdb=" CG2 THR G 34 " pdb=" OE2 GLU K 178 " model vdw 2.033 3.460 nonbonded pdb=" O ASN E 222 " pdb=" NH1 ARG Y 146 " model vdw 2.118 3.120 ... (remaining 334374 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 277 or resid 286 through 450 or resid 501)) selection = (chain 'B' and (resid 3 through 277 or resid 286 through 501)) selection = (chain 'C' and (resid 3 through 277 or resid 286 through 450 or resid 501)) selection = (chain 'D' and (resid 3 through 277 or resid 286 through 450 or resid 501)) } ncs_group { reference = (chain 'E' and (resid 1 through 725 or resid 751 through 814)) selection = (chain 'G' and (resid 1 through 503 or resid 556 through 814)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'U' selection = chain 'X' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.000 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 33.890 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 40159 Z= 0.258 Angle : 0.730 13.892 54339 Z= 0.453 Chirality : 0.044 0.307 6052 Planarity : 0.005 0.068 6995 Dihedral : 14.227 178.410 15089 Min Nonbonded Distance : 1.321 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 0.23 % Allowed : 3.02 % Favored : 96.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.11), residues: 4773 helix: -0.71 (0.09), residues: 2732 sheet: -2.35 (0.25), residues: 356 loop : -2.32 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 630 TYR 0.116 0.002 TYR Y 186 PHE 0.064 0.002 PHE Y 134 TRP 0.015 0.002 TRP D 105 HIS 0.012 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00479 (40155) covalent geometry : angle 0.72980 (54339) hydrogen bonds : bond 0.11947 ( 2274) hydrogen bonds : angle 5.83157 ( 6699) Misc. bond : bond 0.00092 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1313 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASN cc_start: 0.7286 (m110) cc_final: 0.7001 (m110) REVERT: B 125 LYS cc_start: 0.9227 (tttm) cc_final: 0.9024 (tmmt) REVERT: B 134 GLU cc_start: 0.7855 (tp30) cc_final: 0.7534 (tp30) REVERT: B 347 TRP cc_start: 0.7512 (p-90) cc_final: 0.6829 (p-90) REVERT: B 412 LEU cc_start: 0.7433 (tp) cc_final: 0.5796 (tp) REVERT: A 90 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7498 (mtm110) REVERT: A 267 PHE cc_start: 0.7821 (m-80) cc_final: 0.7328 (m-80) REVERT: A 293 ASP cc_start: 0.8347 (m-30) cc_final: 0.8103 (m-30) REVERT: A 422 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7944 (mm-30) REVERT: C 83 PHE cc_start: 0.8323 (m-80) cc_final: 0.8012 (m-80) REVERT: C 125 LYS cc_start: 0.9290 (mmmt) cc_final: 0.9062 (mmtm) REVERT: C 289 HIS cc_start: 0.8249 (m-70) cc_final: 0.8038 (m-70) REVERT: C 293 ASP cc_start: 0.7972 (m-30) cc_final: 0.7408 (m-30) REVERT: C 416 MET cc_start: 0.7673 (tpt) cc_final: 0.7239 (tpt) REVERT: D 173 PHE cc_start: 0.7296 (m-80) cc_final: 0.7044 (m-80) REVERT: D 294 VAL cc_start: 0.9354 (t) cc_final: 0.9072 (t) REVERT: D 298 LEU cc_start: 0.8861 (mt) cc_final: 0.8447 (mp) REVERT: D 305 LEU cc_start: 0.8850 (mt) cc_final: 0.8632 (mt) REVERT: D 308 THR cc_start: 0.5917 (p) cc_final: 0.5486 (p) REVERT: D 378 SER cc_start: 0.8258 (m) cc_final: 0.8037 (p) REVERT: D 452 ASP cc_start: 0.6665 (t0) cc_final: 0.6105 (m-30) REVERT: E 150 TYR cc_start: 0.7881 (t80) cc_final: 0.7669 (t80) REVERT: E 597 ARG cc_start: 0.8358 (tpt170) cc_final: 0.8124 (tpt-90) REVERT: E 624 ARG cc_start: 0.7288 (mmm-85) cc_final: 0.6650 (ttt90) REVERT: F 453 TYR cc_start: 0.8000 (t80) cc_final: 0.7758 (t80) REVERT: F 495 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8496 (mmmm) REVERT: F 615 LYS cc_start: 0.8544 (mttt) cc_final: 0.8341 (mtmm) REVERT: G 594 TYR cc_start: 0.7827 (t80) cc_final: 0.7525 (t80) REVERT: G 709 PHE cc_start: 0.8676 (t80) cc_final: 0.7994 (t80) REVERT: H 835 ASP cc_start: 0.8010 (m-30) cc_final: 0.7751 (m-30) REVERT: H 844 SER cc_start: 0.9355 (t) cc_final: 0.9038 (p) REVERT: U 164 GLU cc_start: -0.0118 (OUTLIER) cc_final: -0.0318 (pm20) REVERT: K 122 GLN cc_start: 0.7593 (tp40) cc_final: 0.7017 (tm-30) REVERT: K 140 SER cc_start: 0.8902 (m) cc_final: 0.8680 (p) outliers start: 10 outliers final: 5 residues processed: 1321 average time/residue: 0.6275 time to fit residues: 1021.7123 Evaluate side-chains 901 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 895 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain G residue 811 ILE Chi-restraints excluded: chain U residue 164 GLU Chi-restraints excluded: chain Y residue 145 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 15 ASN B 153 ASN B 219 ASN B 240 ASN B 303 ASN B 353 HIS B 418 ASN ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 GLN A 81 ASN A 132 ASN A 153 ASN A 240 ASN A 289 HIS A 311 ASN A 317 ASN A 340 GLN A 370 ASN A 385 ASN A 420 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 206 ASN C 225 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN E 175 GLN E 222 ASN E 258 ASN E 379 ASN ** E 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN E 485 GLN E 595 HIS E 607 ASN E 637 ASN E 770 ASN E 781 ASN F 420 GLN F 436 ASN F 459 HIS F 521 GLN F 530 ASN F 588 ASN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN F 728 HIS F 832 ASN G 65 ASN G 227 HIS G 637 ASN ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 673 GLN G 784 GLN H 380 HIS H 436 ASN ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 HIS H 521 GLN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 ASN H 588 ASN H 608 ASN ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 799 ASN Y 157 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093572 restraints weight = 79662.399| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.55 r_work: 0.3144 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 40159 Z= 0.188 Angle : 0.694 15.501 54339 Z= 0.356 Chirality : 0.044 0.210 6052 Planarity : 0.005 0.058 6995 Dihedral : 8.120 178.406 5331 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 3.54 % Allowed : 16.22 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 4773 helix: 0.64 (0.09), residues: 2745 sheet: -1.71 (0.26), residues: 341 loop : -1.67 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 683 TYR 0.029 0.002 TYR E 809 PHE 0.033 0.002 PHE H 641 TRP 0.028 0.002 TRP A 93 HIS 0.013 0.001 HIS G 28 Details of bonding type rmsd covalent geometry : bond 0.00427 (40155) covalent geometry : angle 0.69445 (54339) hydrogen bonds : bond 0.05050 ( 2274) hydrogen bonds : angle 4.87170 ( 6699) Misc. bond : bond 0.00081 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1001 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.6950 (t0) REVERT: B 68 MET cc_start: 0.8486 (mtp) cc_final: 0.8245 (mtt) REVERT: B 69 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7057 (pp-130) REVERT: B 84 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8337 (tpp80) REVERT: B 125 LYS cc_start: 0.9318 (tttm) cc_final: 0.8943 (tmmt) REVERT: B 134 GLU cc_start: 0.8331 (tp30) cc_final: 0.7706 (tp30) REVERT: B 205 ASP cc_start: 0.8310 (t0) cc_final: 0.7974 (t0) REVERT: B 327 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7989 (tm-30) REVERT: B 335 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7533 (tmm) REVERT: B 347 TRP cc_start: 0.7267 (p-90) cc_final: 0.6557 (p-90) REVERT: B 375 MET cc_start: 0.8582 (tmm) cc_final: 0.8374 (tmm) REVERT: B 379 ASN cc_start: 0.6385 (t0) cc_final: 0.5901 (m-40) REVERT: A 47 ASP cc_start: 0.8159 (p0) cc_final: 0.7795 (p0) REVERT: A 88 ASP cc_start: 0.7899 (t0) cc_final: 0.7444 (t0) REVERT: A 90 ARG cc_start: 0.8612 (mtm110) cc_final: 0.8382 (mtm110) REVERT: A 132 ASN cc_start: 0.8323 (t0) cc_final: 0.8069 (t0) REVERT: A 156 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 225 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7367 (pp30) REVERT: A 226 HIS cc_start: 0.7959 (p90) cc_final: 0.7734 (p-80) REVERT: A 422 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8198 (mm-30) REVERT: C 13 CYS cc_start: 0.8890 (t) cc_final: 0.8615 (t) REVERT: C 41 ASP cc_start: 0.8561 (p0) cc_final: 0.8207 (t0) REVERT: C 49 ASP cc_start: 0.8617 (t0) cc_final: 0.8413 (t0) REVERT: C 69 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7546 (mpp) REVERT: C 83 PHE cc_start: 0.8747 (m-80) cc_final: 0.8295 (m-80) REVERT: C 125 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9117 (mptt) REVERT: C 130 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8507 (p) REVERT: C 166 ILE cc_start: 0.9363 (mp) cc_final: 0.8224 (mp) REVERT: C 185 TYR cc_start: 0.9057 (m-80) cc_final: 0.8701 (m-80) REVERT: C 206 ASN cc_start: 0.9375 (OUTLIER) cc_final: 0.8893 (m110) REVERT: C 258 THR cc_start: 0.9402 (m) cc_final: 0.9103 (p) REVERT: C 275 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7496 (p90) REVERT: C 355 ASN cc_start: 0.9165 (t0) cc_final: 0.8956 (t0) REVERT: C 378 SER cc_start: 0.9426 (OUTLIER) cc_final: 0.8568 (t) REVERT: C 434 MET cc_start: 0.8665 (mtm) cc_final: 0.8399 (mtm) REVERT: C 441 GLU cc_start: 0.8870 (tt0) cc_final: 0.8634 (tt0) REVERT: D 27 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8620 (mmtm) REVERT: D 36 LEU cc_start: 0.8771 (mm) cc_final: 0.8556 (mm) REVERT: D 138 LEU cc_start: 0.7050 (tt) cc_final: 0.6519 (mp) REVERT: D 155 LEU cc_start: 0.9204 (mt) cc_final: 0.9002 (mt) REVERT: D 165 LYS cc_start: 0.8646 (mmmt) cc_final: 0.7973 (mmtm) REVERT: D 173 PHE cc_start: 0.7594 (m-80) cc_final: 0.7166 (m-80) REVERT: D 252 MET cc_start: 0.7843 (mmm) cc_final: 0.7402 (mmm) REVERT: D 286 HIS cc_start: 0.6019 (OUTLIER) cc_final: 0.5619 (m-70) REVERT: D 289 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.8784 (p-80) REVERT: D 298 LEU cc_start: 0.8917 (mt) cc_final: 0.8507 (mp) REVERT: D 305 LEU cc_start: 0.8667 (mt) cc_final: 0.8429 (mt) REVERT: D 308 THR cc_start: 0.6582 (p) cc_final: 0.5926 (p) REVERT: D 376 MET cc_start: 0.9029 (ttp) cc_final: 0.8758 (ttp) REVERT: D 378 SER cc_start: 0.8515 (m) cc_final: 0.7828 (p) REVERT: D 434 MET cc_start: 0.7101 (mmt) cc_final: 0.6785 (mtt) REVERT: D 441 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7892 (mp0) REVERT: D 452 ASP cc_start: 0.6173 (t0) cc_final: 0.5741 (t0) REVERT: E 2 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7981 (mp0) REVERT: E 14 ARG cc_start: 0.8141 (ppp-140) cc_final: 0.7872 (tmm-80) REVERT: E 28 HIS cc_start: 0.8047 (t-90) cc_final: 0.7844 (t-90) REVERT: E 90 ILE cc_start: 0.9581 (mt) cc_final: 0.9352 (mp) REVERT: E 147 GLU cc_start: 0.8708 (tt0) cc_final: 0.8428 (tt0) REVERT: E 150 TYR cc_start: 0.9299 (t80) cc_final: 0.9092 (t80) REVERT: E 331 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8994 (mm) REVERT: E 338 GLU cc_start: 0.8840 (tt0) cc_final: 0.8538 (pm20) REVERT: E 460 LYS cc_start: 0.8965 (tttp) cc_final: 0.8374 (pptt) REVERT: E 464 ASN cc_start: 0.9600 (m-40) cc_final: 0.9377 (m110) REVERT: E 597 ARG cc_start: 0.8746 (tpt170) cc_final: 0.8314 (tpt-90) REVERT: E 607 ASN cc_start: 0.8662 (m-40) cc_final: 0.8432 (m110) REVERT: E 653 ASP cc_start: 0.6893 (m-30) cc_final: 0.6630 (m-30) REVERT: E 687 ARG cc_start: 0.7727 (mpp-170) cc_final: 0.7471 (mmp-170) REVERT: E 698 GLN cc_start: 0.7856 (tt0) cc_final: 0.7631 (pt0) REVERT: E 809 TYR cc_start: 0.8423 (m-80) cc_final: 0.7869 (m-80) REVERT: F 264 TYR cc_start: 0.9441 (t80) cc_final: 0.9205 (t80) REVERT: F 380 HIS cc_start: 0.9065 (OUTLIER) cc_final: 0.8784 (t70) REVERT: F 396 LYS cc_start: 0.9078 (pmtt) cc_final: 0.8833 (pmtt) REVERT: F 490 ASP cc_start: 0.8509 (m-30) cc_final: 0.7830 (m-30) REVERT: F 512 LEU cc_start: 0.9283 (mt) cc_final: 0.9050 (mm) REVERT: F 517 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8869 (pt0) REVERT: F 615 LYS cc_start: 0.8696 (mttt) cc_final: 0.8259 (mtmm) REVERT: F 651 TYR cc_start: 0.9183 (t80) cc_final: 0.8843 (t80) REVERT: F 656 ILE cc_start: 0.8993 (mp) cc_final: 0.8748 (mp) REVERT: F 660 ASN cc_start: 0.9125 (m110) cc_final: 0.8853 (m-40) REVERT: F 662 LYS cc_start: 0.9322 (ttmm) cc_final: 0.9048 (ttmm) REVERT: F 663 GLU cc_start: 0.8881 (tp30) cc_final: 0.8678 (tp30) REVERT: F 717 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8380 (tmmm) REVERT: F 723 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8870 (mt-10) REVERT: F 845 LEU cc_start: 0.8244 (mt) cc_final: 0.8018 (mt) REVERT: G 144 ARG cc_start: 0.8943 (mtp85) cc_final: 0.8432 (tpp-160) REVERT: G 584 ILE cc_start: 0.9161 (mp) cc_final: 0.8957 (tt) REVERT: G 594 TYR cc_start: 0.9203 (t80) cc_final: 0.8517 (t80) REVERT: G 645 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8821 (tt0) REVERT: G 709 PHE cc_start: 0.8950 (t80) cc_final: 0.8525 (t80) REVERT: H 289 GLU cc_start: 0.8727 (tp30) cc_final: 0.8130 (tp30) REVERT: H 315 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8394 (mm-30) REVERT: H 420 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8468 (tm-30) REVERT: H 439 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8271 (mtp180) REVERT: H 489 MET cc_start: 0.7963 (mmm) cc_final: 0.7604 (mmm) REVERT: H 529 MET cc_start: 0.8727 (tmm) cc_final: 0.8466 (tmm) REVERT: H 642 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7646 (tm-30) REVERT: H 661 PHE cc_start: 0.8182 (t80) cc_final: 0.7970 (t80) REVERT: H 666 ARG cc_start: 0.9233 (ptp90) cc_final: 0.8996 (ptp90) REVERT: H 690 GLU cc_start: 0.8226 (pp20) cc_final: 0.7890 (pp20) REVERT: H 691 LEU cc_start: 0.8730 (tp) cc_final: 0.8436 (tm) REVERT: H 717 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7887 (tmmt) REVERT: H 725 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8457 (tp30) REVERT: H 812 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8249 (pp) REVERT: H 835 ASP cc_start: 0.8877 (m-30) cc_final: 0.8380 (m-30) REVERT: H 841 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8655 (pp) REVERT: H 844 SER cc_start: 0.9287 (t) cc_final: 0.8919 (p) REVERT: K 122 GLN cc_start: 0.8468 (tp40) cc_final: 0.8212 (tm-30) REVERT: K 126 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8714 (mm-30) REVERT: K 140 SER cc_start: 0.8961 (m) cc_final: 0.8722 (p) REVERT: Y 119 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6893 (mm) REVERT: Y 125 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8490 (ttm110) REVERT: Y 133 ARG cc_start: 0.8989 (mtm-85) cc_final: 0.8605 (ttm110) outliers start: 157 outliers final: 44 residues processed: 1069 average time/residue: 0.5979 time to fit residues: 799.0604 Evaluate side-chains 922 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 859 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain E residue 663 TYR Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 379 TYR Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 486 SER Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 643 GLN Chi-restraints excluded: chain F residue 647 LYS Chi-restraints excluded: chain F residue 717 LYS Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 423 ASN Chi-restraints excluded: chain H residue 538 ILE Chi-restraints excluded: chain H residue 541 LEU Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 717 LYS Chi-restraints excluded: chain H residue 725 GLU Chi-restraints excluded: chain H residue 812 ILE Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 289 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 292 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 196 optimal weight: 0.5980 chunk 297 optimal weight: 0.6980 chunk 300 optimal weight: 0.0870 chunk 433 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 207 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN B 91 ASN B 153 ASN B 303 ASN ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 221 ASN D 340 GLN E 222 ASN E 421 HIS E 589 GLN F 222 HIS F 262 GLN F 469 HIS F 521 GLN ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 ASN ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 521 GLN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 ASN H 608 ASN ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.137164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.095220 restraints weight = 79433.720| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.58 r_work: 0.3177 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40159 Z= 0.145 Angle : 0.650 21.092 54339 Z= 0.329 Chirality : 0.043 0.208 6052 Planarity : 0.004 0.053 6995 Dihedral : 7.900 177.991 5318 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.27 % Allowed : 19.27 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4773 helix: 1.13 (0.10), residues: 2739 sheet: -1.39 (0.28), residues: 340 loop : -1.28 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 204 TYR 0.024 0.001 TYR A 292 PHE 0.040 0.002 PHE H 641 TRP 0.024 0.002 TRP A 93 HIS 0.007 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00319 (40155) covalent geometry : angle 0.64966 (54339) hydrogen bonds : bond 0.04637 ( 2274) hydrogen bonds : angle 4.68183 ( 6699) Misc. bond : bond 0.00066 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1021 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 LEU cc_start: 0.9111 (mm) cc_final: 0.8590 (pt) REVERT: B 47 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7025 (t0) REVERT: B 62 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8986 (m-10) REVERT: B 103 ASN cc_start: 0.7875 (m-40) cc_final: 0.7320 (t0) REVERT: B 125 LYS cc_start: 0.9308 (tttm) cc_final: 0.8812 (pttm) REVERT: B 287 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5965 (tptt) REVERT: B 299 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8374 (tt) REVERT: B 347 TRP cc_start: 0.7157 (p-90) cc_final: 0.6413 (p-90) REVERT: A 47 ASP cc_start: 0.8334 (p0) cc_final: 0.7840 (p0) REVERT: A 74 SER cc_start: 0.9243 (t) cc_final: 0.9015 (p) REVERT: A 88 ASP cc_start: 0.7974 (t0) cc_final: 0.7434 (t0) REVERT: A 90 ARG cc_start: 0.8670 (mtm110) cc_final: 0.8407 (mtm110) REVERT: A 120 LEU cc_start: 0.8682 (mm) cc_final: 0.8248 (mp) REVERT: A 124 ASP cc_start: 0.9086 (t0) cc_final: 0.8700 (m-30) REVERT: A 132 ASN cc_start: 0.8575 (t0) cc_final: 0.8373 (t0) REVERT: A 156 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8498 (mm-30) REVERT: A 161 ARG cc_start: 0.9207 (ttt90) cc_final: 0.8951 (ttm170) REVERT: A 167 LEU cc_start: 0.9528 (mm) cc_final: 0.9299 (mm) REVERT: A 267 PHE cc_start: 0.8854 (m-80) cc_final: 0.7909 (m-80) REVERT: A 272 PHE cc_start: 0.8816 (t80) cc_final: 0.8519 (t80) REVERT: A 375 MET cc_start: 0.9350 (tmm) cc_final: 0.9061 (tmm) REVERT: A 422 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 13 CYS cc_start: 0.8864 (t) cc_final: 0.8637 (t) REVERT: C 19 LYS cc_start: 0.9355 (ttmm) cc_final: 0.8864 (ttpp) REVERT: C 41 ASP cc_start: 0.8483 (p0) cc_final: 0.8176 (t0) REVERT: C 47 ASP cc_start: 0.8912 (m-30) cc_final: 0.8369 (p0) REVERT: C 49 ASP cc_start: 0.8612 (t0) cc_final: 0.8365 (t0) REVERT: C 69 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7486 (mpp) REVERT: C 83 PHE cc_start: 0.8764 (m-80) cc_final: 0.8139 (m-80) REVERT: C 125 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9037 (mmtm) REVERT: C 156 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8464 (mm-30) REVERT: C 165 LYS cc_start: 0.8742 (mmtt) cc_final: 0.7955 (mmmm) REVERT: C 185 TYR cc_start: 0.9032 (m-80) cc_final: 0.8579 (m-80) REVERT: C 187 THR cc_start: 0.9030 (m) cc_final: 0.8745 (p) REVERT: C 196 GLU cc_start: 0.7644 (pp20) cc_final: 0.7278 (pp20) REVERT: C 343 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8649 (ttpm) REVERT: C 352 MET cc_start: 0.8358 (mpp) cc_final: 0.8133 (mpt) REVERT: C 434 MET cc_start: 0.8700 (mtm) cc_final: 0.8446 (mtm) REVERT: C 441 GLU cc_start: 0.8831 (tt0) cc_final: 0.8531 (tt0) REVERT: D 27 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8631 (mmtm) REVERT: D 36 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8522 (mm) REVERT: D 69 MET cc_start: 0.6461 (pmm) cc_final: 0.6242 (pmm) REVERT: D 110 ASP cc_start: 0.7794 (t0) cc_final: 0.7266 (t0) REVERT: D 155 LEU cc_start: 0.9187 (mt) cc_final: 0.8914 (mt) REVERT: D 165 LYS cc_start: 0.8678 (mmmt) cc_final: 0.7978 (mmtm) REVERT: D 252 MET cc_start: 0.7771 (mmm) cc_final: 0.7334 (mmm) REVERT: D 289 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.8699 (p-80) REVERT: D 298 LEU cc_start: 0.8917 (mt) cc_final: 0.8527 (mp) REVERT: D 305 LEU cc_start: 0.8574 (mt) cc_final: 0.8356 (mt) REVERT: D 308 THR cc_start: 0.6703 (p) cc_final: 0.6259 (p) REVERT: D 321 THR cc_start: 0.8885 (m) cc_final: 0.8444 (p) REVERT: D 329 ARG cc_start: 0.8330 (tpm-80) cc_final: 0.8085 (tpm-80) REVERT: D 375 MET cc_start: 0.8838 (tmm) cc_final: 0.8552 (tmm) REVERT: D 376 MET cc_start: 0.8918 (ttp) cc_final: 0.8655 (ttp) REVERT: D 378 SER cc_start: 0.8585 (m) cc_final: 0.7817 (p) REVERT: D 434 MET cc_start: 0.7122 (mmt) cc_final: 0.6752 (mtt) REVERT: D 441 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7948 (mp0) REVERT: D 452 ASP cc_start: 0.6134 (t0) cc_final: 0.5719 (t0) REVERT: E 2 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7980 (mp0) REVERT: E 14 ARG cc_start: 0.8129 (ppp-140) cc_final: 0.7736 (ptm160) REVERT: E 148 ASP cc_start: 0.8887 (m-30) cc_final: 0.8521 (m-30) REVERT: E 201 GLU cc_start: 0.8441 (pp20) cc_final: 0.8074 (pp20) REVERT: E 331 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8912 (mm) REVERT: E 338 GLU cc_start: 0.8823 (tt0) cc_final: 0.8599 (pm20) REVERT: E 383 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8261 (t0) REVERT: E 441 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8053 (ptpp) REVERT: E 460 LYS cc_start: 0.9092 (tttp) cc_final: 0.8538 (pptt) REVERT: E 469 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8722 (ttp80) REVERT: E 473 ASN cc_start: 0.8644 (t0) cc_final: 0.8340 (t0) REVERT: E 485 GLN cc_start: 0.8765 (mt0) cc_final: 0.8315 (mp10) REVERT: E 597 ARG cc_start: 0.8733 (tpt170) cc_final: 0.8361 (tpt-90) REVERT: E 624 ARG cc_start: 0.6717 (mtp85) cc_final: 0.6517 (ttt90) REVERT: E 674 ASN cc_start: 0.9132 (m-40) cc_final: 0.8802 (m-40) REVERT: E 809 TYR cc_start: 0.8463 (m-80) cc_final: 0.7843 (m-80) REVERT: F 264 TYR cc_start: 0.9424 (t80) cc_final: 0.9127 (t80) REVERT: F 380 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8739 (t70) REVERT: F 396 LYS cc_start: 0.9111 (pmtt) cc_final: 0.8863 (pmtt) REVERT: F 512 LEU cc_start: 0.9346 (mt) cc_final: 0.9109 (mm) REVERT: F 517 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8860 (pt0) REVERT: F 615 LYS cc_start: 0.8683 (mttt) cc_final: 0.8246 (mtmm) REVERT: F 651 TYR cc_start: 0.9160 (t80) cc_final: 0.8851 (t80) REVERT: F 659 GLU cc_start: 0.8879 (tp30) cc_final: 0.8620 (mm-30) REVERT: F 662 LYS cc_start: 0.9292 (ttmm) cc_final: 0.9065 (ttmm) REVERT: F 663 GLU cc_start: 0.9022 (tp30) cc_final: 0.8815 (tp30) REVERT: F 669 GLN cc_start: 0.8773 (mp10) cc_final: 0.8172 (tm-30) REVERT: F 680 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8319 (p0) REVERT: F 689 ILE cc_start: 0.8995 (mt) cc_final: 0.8771 (mp) REVERT: F 691 LEU cc_start: 0.8887 (tt) cc_final: 0.8412 (tt) REVERT: F 717 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8477 (tmmm) REVERT: F 726 SER cc_start: 0.9417 (t) cc_final: 0.9094 (p) REVERT: G 144 ARG cc_start: 0.8943 (mtp85) cc_final: 0.8593 (mmt-90) REVERT: G 468 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8962 (mt-10) REVERT: G 487 ASP cc_start: 0.8741 (t0) cc_final: 0.8490 (t0) REVERT: G 594 TYR cc_start: 0.9187 (t80) cc_final: 0.8573 (t80) REVERT: G 604 MET cc_start: 0.9065 (mmm) cc_final: 0.8825 (mmm) REVERT: G 645 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8855 (tt0) REVERT: H 289 GLU cc_start: 0.8684 (tp30) cc_final: 0.8224 (tp30) REVERT: H 315 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8274 (mm-30) REVERT: H 420 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8399 (tm-30) REVERT: H 439 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8154 (mtp180) REVERT: H 529 MET cc_start: 0.8694 (tmm) cc_final: 0.8365 (tmm) REVERT: H 592 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.7261 (mtt180) REVERT: H 647 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8494 (tptt) REVERT: H 662 LYS cc_start: 0.9372 (tppp) cc_final: 0.8811 (tptp) REVERT: H 690 GLU cc_start: 0.8065 (pp20) cc_final: 0.7670 (pp20) REVERT: H 691 LEU cc_start: 0.8703 (tp) cc_final: 0.8351 (tm) REVERT: H 725 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: H 817 LYS cc_start: 0.8942 (tptp) cc_final: 0.8720 (mmmt) REVERT: H 821 ASP cc_start: 0.8577 (m-30) cc_final: 0.8353 (m-30) REVERT: H 835 ASP cc_start: 0.8815 (m-30) cc_final: 0.8397 (m-30) REVERT: H 836 GLU cc_start: 0.9031 (tt0) cc_final: 0.8487 (tm-30) REVERT: H 844 SER cc_start: 0.9298 (t) cc_final: 0.8885 (p) REVERT: K 115 MET cc_start: 0.8103 (ptt) cc_final: 0.7754 (ptt) REVERT: K 122 GLN cc_start: 0.8472 (tp40) cc_final: 0.8022 (tm-30) REVERT: K 126 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8605 (mm-30) REVERT: K 130 LYS cc_start: 0.9367 (ttmt) cc_final: 0.8922 (tttp) REVERT: K 136 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8650 (ttm-80) REVERT: K 149 THR cc_start: 0.6440 (p) cc_final: 0.6164 (p) REVERT: Y 119 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6682 (mm) REVERT: Y 125 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8499 (ttm110) outliers start: 145 outliers final: 40 residues processed: 1076 average time/residue: 0.6525 time to fit residues: 869.8061 Evaluate side-chains 941 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 885 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 486 SER Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 643 GLN Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 696 THR Chi-restraints excluded: chain F residue 717 LYS Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 277 VAL Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 423 ASN Chi-restraints excluded: chain H residue 647 LYS Chi-restraints excluded: chain H residue 725 GLU Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 388 optimal weight: 0.5980 chunk 396 optimal weight: 0.9980 chunk 306 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 364 optimal weight: 0.9990 chunk 307 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN A 9 GLN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN D 340 GLN E 222 ASN E 607 ASN E 686 ASN F 608 ASN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 HIS ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 673 GLN H 169 GLN ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 521 GLN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 738 HIS Y 122 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094898 restraints weight = 79466.117| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.57 r_work: 0.3166 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 40159 Z= 0.166 Angle : 0.662 14.625 54339 Z= 0.330 Chirality : 0.044 0.304 6052 Planarity : 0.004 0.065 6995 Dihedral : 7.830 178.352 5318 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.81 % Allowed : 21.02 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 4773 helix: 1.29 (0.10), residues: 2743 sheet: -1.14 (0.27), residues: 354 loop : -1.11 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 204 TYR 0.037 0.002 TYR G 725 PHE 0.038 0.002 PHE H 641 TRP 0.023 0.002 TRP E 320 HIS 0.010 0.001 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00378 (40155) covalent geometry : angle 0.66186 (54339) hydrogen bonds : bond 0.04559 ( 2274) hydrogen bonds : angle 4.62053 ( 6699) Misc. bond : bond 0.00056 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 966 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 LEU cc_start: 0.9117 (mm) cc_final: 0.8586 (pt) REVERT: B 47 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7019 (t0) REVERT: B 84 ARG cc_start: 0.8848 (mmm160) cc_final: 0.8388 (tpp80) REVERT: B 103 ASN cc_start: 0.7902 (m-40) cc_final: 0.7372 (t0) REVERT: B 125 LYS cc_start: 0.9301 (tttm) cc_final: 0.8799 (pttm) REVERT: B 169 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8482 (t) REVERT: B 287 LYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5936 (tptt) REVERT: B 327 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 333 ARG cc_start: 0.9200 (mmt90) cc_final: 0.8978 (mmt90) REVERT: B 347 TRP cc_start: 0.7181 (p-90) cc_final: 0.6377 (p-90) REVERT: A 47 ASP cc_start: 0.8396 (p0) cc_final: 0.7796 (p0) REVERT: A 74 SER cc_start: 0.9299 (t) cc_final: 0.9047 (p) REVERT: A 88 ASP cc_start: 0.8011 (t0) cc_final: 0.7472 (t0) REVERT: A 90 ARG cc_start: 0.8693 (mtm110) cc_final: 0.8433 (mtm110) REVERT: A 93 TRP cc_start: 0.8306 (t60) cc_final: 0.8033 (t60) REVERT: A 132 ASN cc_start: 0.8628 (t0) cc_final: 0.8385 (t0) REVERT: A 156 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8552 (mm-30) REVERT: A 167 LEU cc_start: 0.9506 (mm) cc_final: 0.9237 (mm) REVERT: A 252 MET cc_start: 0.9279 (mmm) cc_final: 0.9030 (mmm) REVERT: A 267 PHE cc_start: 0.8907 (m-80) cc_final: 0.8027 (m-80) REVERT: A 272 PHE cc_start: 0.8901 (t80) cc_final: 0.8649 (t80) REVERT: A 422 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8253 (mm-30) REVERT: C 13 CYS cc_start: 0.9061 (t) cc_final: 0.8726 (t) REVERT: C 19 LYS cc_start: 0.9371 (ttmm) cc_final: 0.8888 (ttpp) REVERT: C 41 ASP cc_start: 0.8444 (p0) cc_final: 0.8204 (t0) REVERT: C 47 ASP cc_start: 0.8990 (m-30) cc_final: 0.8458 (p0) REVERT: C 49 ASP cc_start: 0.8619 (t0) cc_final: 0.8397 (t0) REVERT: C 69 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7757 (mpp) REVERT: C 83 PHE cc_start: 0.8813 (m-80) cc_final: 0.8225 (m-80) REVERT: C 124 ASP cc_start: 0.8955 (t0) cc_final: 0.8708 (t0) REVERT: C 125 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9064 (mptt) REVERT: C 156 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8471 (mm-30) REVERT: C 165 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8093 (mmmm) REVERT: C 185 TYR cc_start: 0.9049 (m-80) cc_final: 0.8637 (m-80) REVERT: C 187 THR cc_start: 0.9016 (m) cc_final: 0.8732 (p) REVERT: C 196 GLU cc_start: 0.7706 (pp20) cc_final: 0.7427 (pp20) REVERT: C 343 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8642 (ttpm) REVERT: C 396 LYS cc_start: 0.8855 (mppt) cc_final: 0.8466 (mmtm) REVERT: C 434 MET cc_start: 0.8674 (mtm) cc_final: 0.8360 (mtm) REVERT: C 441 GLU cc_start: 0.8823 (tt0) cc_final: 0.8546 (tt0) REVERT: D 27 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8737 (mmtm) REVERT: D 36 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8518 (mm) REVERT: D 110 ASP cc_start: 0.7764 (t0) cc_final: 0.7230 (t0) REVERT: D 138 LEU cc_start: 0.7039 (tm) cc_final: 0.6746 (mp) REVERT: D 155 LEU cc_start: 0.9216 (mt) cc_final: 0.8974 (mt) REVERT: D 165 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8070 (mppt) REVERT: D 252 MET cc_start: 0.7796 (mmm) cc_final: 0.7429 (mmt) REVERT: D 286 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5765 (m-70) REVERT: D 308 THR cc_start: 0.6688 (p) cc_final: 0.6349 (p) REVERT: D 342 ILE cc_start: 0.8396 (mt) cc_final: 0.8196 (mt) REVERT: D 376 MET cc_start: 0.8830 (ttp) cc_final: 0.8578 (ttp) REVERT: D 378 SER cc_start: 0.8575 (m) cc_final: 0.7750 (p) REVERT: D 434 MET cc_start: 0.7177 (mmt) cc_final: 0.6939 (mtt) REVERT: D 441 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8003 (mp0) REVERT: D 452 ASP cc_start: 0.6214 (t0) cc_final: 0.5828 (t0) REVERT: E 2 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8013 (mp0) REVERT: E 14 ARG cc_start: 0.8105 (ppp-140) cc_final: 0.7695 (ptm160) REVERT: E 201 GLU cc_start: 0.8362 (pp20) cc_final: 0.8044 (pp20) REVERT: E 331 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8962 (mm) REVERT: E 338 GLU cc_start: 0.8850 (tt0) cc_final: 0.8606 (pm20) REVERT: E 383 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8138 (t0) REVERT: E 469 ARG cc_start: 0.9138 (ttp80) cc_final: 0.8738 (ttp80) REVERT: E 473 ASN cc_start: 0.8690 (t0) cc_final: 0.8396 (t0) REVERT: E 485 GLN cc_start: 0.8793 (mt0) cc_final: 0.8311 (mp10) REVERT: E 648 ASN cc_start: 0.8687 (m-40) cc_final: 0.8295 (m110) REVERT: E 674 ASN cc_start: 0.9129 (m-40) cc_final: 0.8760 (m-40) REVERT: E 687 ARG cc_start: 0.7936 (mpp-170) cc_final: 0.7735 (mpp-170) REVERT: E 698 GLN cc_start: 0.8090 (tt0) cc_final: 0.7650 (pt0) REVERT: E 710 ILE cc_start: 0.8871 (mm) cc_final: 0.8605 (mp) REVERT: E 809 TYR cc_start: 0.8571 (m-80) cc_final: 0.7951 (m-80) REVERT: F 264 TYR cc_start: 0.9444 (t80) cc_final: 0.9243 (t80) REVERT: F 380 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8628 (t70) REVERT: F 397 GLU cc_start: 0.8576 (mp0) cc_final: 0.8297 (mp0) REVERT: F 490 ASP cc_start: 0.8378 (m-30) cc_final: 0.8011 (m-30) REVERT: F 512 LEU cc_start: 0.9351 (mt) cc_final: 0.9150 (mm) REVERT: F 517 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8870 (pt0) REVERT: F 527 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8764 (m170) REVERT: F 528 LEU cc_start: 0.9180 (tp) cc_final: 0.8834 (tp) REVERT: F 615 LYS cc_start: 0.8687 (mttt) cc_final: 0.8252 (mtmm) REVERT: F 651 TYR cc_start: 0.9206 (t80) cc_final: 0.8918 (t80) REVERT: F 659 GLU cc_start: 0.8910 (tp30) cc_final: 0.8547 (mm-30) REVERT: F 662 LYS cc_start: 0.9287 (ttmm) cc_final: 0.9023 (ttmm) REVERT: F 663 GLU cc_start: 0.9078 (tp30) cc_final: 0.8786 (tp30) REVERT: F 680 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8157 (p0) REVERT: F 692 ASN cc_start: 0.8610 (t0) cc_final: 0.8346 (t0) REVERT: F 717 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8466 (tmmm) REVERT: F 726 SER cc_start: 0.9409 (t) cc_final: 0.9096 (p) REVERT: F 816 TYR cc_start: 0.8816 (t80) cc_final: 0.8610 (t80) REVERT: F 820 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8637 (mmtp) REVERT: G 144 ARG cc_start: 0.8956 (mtp85) cc_final: 0.8693 (mmt-90) REVERT: G 161 ASP cc_start: 0.8847 (m-30) cc_final: 0.8557 (m-30) REVERT: G 172 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: G 342 ASN cc_start: 0.8997 (m-40) cc_final: 0.8380 (t0) REVERT: G 450 TYR cc_start: 0.8034 (m-10) cc_final: 0.7515 (m-10) REVERT: G 487 ASP cc_start: 0.8777 (t0) cc_final: 0.8519 (t0) REVERT: G 582 TYR cc_start: 0.9355 (m-10) cc_final: 0.9094 (m-80) REVERT: G 594 TYR cc_start: 0.9200 (t80) cc_final: 0.8616 (t80) REVERT: G 645 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8793 (tt0) REVERT: G 709 PHE cc_start: 0.8917 (t80) cc_final: 0.8603 (t80) REVERT: G 806 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8513 (ptp-170) REVERT: H 226 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: H 289 GLU cc_start: 0.8716 (tp30) cc_final: 0.8294 (tp30) REVERT: H 315 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8251 (mm-30) REVERT: H 420 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8407 (tm-30) REVERT: H 529 MET cc_start: 0.8735 (tmm) cc_final: 0.8437 (tmm) REVERT: H 592 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7168 (mtm180) REVERT: H 647 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8503 (tptt) REVERT: H 662 LYS cc_start: 0.9397 (tppp) cc_final: 0.8930 (tptp) REVERT: H 690 GLU cc_start: 0.8074 (pp20) cc_final: 0.7721 (pp20) REVERT: H 691 LEU cc_start: 0.8710 (tp) cc_final: 0.8364 (tm) REVERT: H 717 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8115 (tmmt) REVERT: H 725 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8524 (tp30) REVERT: H 809 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8751 (tm) REVERT: H 835 ASP cc_start: 0.8798 (m-30) cc_final: 0.8339 (m-30) REVERT: H 836 GLU cc_start: 0.9041 (tt0) cc_final: 0.8519 (tm-30) REVERT: H 844 SER cc_start: 0.9328 (t) cc_final: 0.8927 (p) REVERT: K 115 MET cc_start: 0.8083 (ptt) cc_final: 0.7742 (ptt) REVERT: K 122 GLN cc_start: 0.8480 (tp40) cc_final: 0.7978 (tm-30) REVERT: K 126 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8560 (mm-30) REVERT: K 130 LYS cc_start: 0.9424 (ttmt) cc_final: 0.9015 (tttp) REVERT: K 136 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8734 (tpp80) REVERT: K 149 THR cc_start: 0.6482 (p) cc_final: 0.6217 (p) REVERT: Y 129 MET cc_start: 0.8697 (tmt) cc_final: 0.8414 (tpt) outliers start: 169 outliers final: 56 residues processed: 1046 average time/residue: 0.6443 time to fit residues: 839.3573 Evaluate side-chains 936 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 860 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 247 TYR Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain E residue 663 TYR Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 486 SER Chi-restraints excluded: chain F residue 527 HIS Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 643 GLN Chi-restraints excluded: chain F residue 647 LYS Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 696 THR Chi-restraints excluded: chain F residue 717 LYS Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 806 ARG Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 226 GLU Chi-restraints excluded: chain H residue 277 VAL Chi-restraints excluded: chain H residue 339 ILE Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 423 ASN Chi-restraints excluded: chain H residue 647 LYS Chi-restraints excluded: chain H residue 717 LYS Chi-restraints excluded: chain H residue 725 GLU Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 120 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 6 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 227 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 371 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 423 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN D 286 HIS E 222 ASN E 442 ASN E 589 GLN E 607 ASN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 673 GLN G 696 GLN ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 521 GLN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.136457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095021 restraints weight = 79123.725| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.51 r_work: 0.3162 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40159 Z= 0.174 Angle : 0.671 15.381 54339 Z= 0.333 Chirality : 0.044 0.428 6052 Planarity : 0.004 0.057 6995 Dihedral : 7.797 178.416 5316 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.94 % Allowed : 22.35 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.12), residues: 4773 helix: 1.36 (0.10), residues: 2750 sheet: -1.00 (0.27), residues: 362 loop : -0.99 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 439 TYR 0.026 0.002 TYR E 568 PHE 0.052 0.002 PHE H 641 TRP 0.025 0.002 TRP E 320 HIS 0.010 0.001 HIS G 28 Details of bonding type rmsd covalent geometry : bond 0.00395 (40155) covalent geometry : angle 0.67147 (54339) hydrogen bonds : bond 0.04509 ( 2274) hydrogen bonds : angle 4.58541 ( 6699) Misc. bond : bond 0.00056 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 941 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 LEU cc_start: 0.9117 (mm) cc_final: 0.8580 (pt) REVERT: B 47 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7028 (t0) REVERT: B 84 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8306 (tpp80) REVERT: B 125 LYS cc_start: 0.9300 (tttm) cc_final: 0.8825 (ttpp) REVERT: B 169 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8498 (t) REVERT: B 287 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.6023 (tptt) REVERT: B 327 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7529 (tm-30) REVERT: B 347 TRP cc_start: 0.7153 (p-90) cc_final: 0.6368 (p-90) REVERT: A 47 ASP cc_start: 0.8409 (p0) cc_final: 0.7803 (p0) REVERT: A 55 ARG cc_start: 0.8738 (ttp-110) cc_final: 0.8455 (ttp80) REVERT: A 74 SER cc_start: 0.9277 (t) cc_final: 0.9029 (p) REVERT: A 88 ASP cc_start: 0.8006 (t0) cc_final: 0.7528 (t0) REVERT: A 90 ARG cc_start: 0.8680 (mtm110) cc_final: 0.8428 (mtm110) REVERT: A 124 ASP cc_start: 0.9028 (t0) cc_final: 0.8672 (m-30) REVERT: A 125 LYS cc_start: 0.9427 (tppt) cc_final: 0.9071 (tppt) REVERT: A 132 ASN cc_start: 0.8709 (t0) cc_final: 0.8475 (t0) REVERT: A 156 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8555 (mm-30) REVERT: A 167 LEU cc_start: 0.9465 (mm) cc_final: 0.9126 (mm) REVERT: A 252 MET cc_start: 0.9311 (mmm) cc_final: 0.9062 (mmm) REVERT: A 272 PHE cc_start: 0.8906 (t80) cc_final: 0.8607 (t80) REVERT: A 422 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8237 (mm-30) REVERT: C 13 CYS cc_start: 0.9056 (t) cc_final: 0.8733 (t) REVERT: C 19 LYS cc_start: 0.9364 (ttmm) cc_final: 0.8896 (ttpp) REVERT: C 36 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8632 (mm) REVERT: C 47 ASP cc_start: 0.8991 (m-30) cc_final: 0.8604 (p0) REVERT: C 49 ASP cc_start: 0.8666 (t0) cc_final: 0.8437 (t0) REVERT: C 69 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7611 (mmm) REVERT: C 83 PHE cc_start: 0.8791 (m-80) cc_final: 0.8226 (m-80) REVERT: C 124 ASP cc_start: 0.8989 (t0) cc_final: 0.8765 (t0) REVERT: C 125 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9034 (mptt) REVERT: C 156 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8513 (mm-30) REVERT: C 187 THR cc_start: 0.8987 (m) cc_final: 0.8698 (p) REVERT: C 196 GLU cc_start: 0.7781 (pp20) cc_final: 0.7510 (pp20) REVERT: C 264 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: C 343 LYS cc_start: 0.9021 (ttpp) cc_final: 0.8617 (ttpm) REVERT: C 396 LYS cc_start: 0.8854 (mppt) cc_final: 0.8545 (mppt) REVERT: C 434 MET cc_start: 0.8785 (mtm) cc_final: 0.8441 (mtm) REVERT: D 27 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8737 (mmtm) REVERT: D 36 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8541 (mm) REVERT: D 110 ASP cc_start: 0.7815 (t0) cc_final: 0.7289 (t0) REVERT: D 138 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6796 (mp) REVERT: D 155 LEU cc_start: 0.9219 (mt) cc_final: 0.8965 (mt) REVERT: D 165 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8295 (mmmm) REVERT: D 252 MET cc_start: 0.7767 (mmm) cc_final: 0.7336 (mmm) REVERT: D 298 LEU cc_start: 0.8881 (mt) cc_final: 0.8675 (mt) REVERT: D 308 THR cc_start: 0.6723 (p) cc_final: 0.6429 (p) REVERT: D 321 THR cc_start: 0.9025 (m) cc_final: 0.8580 (p) REVERT: D 342 ILE cc_start: 0.8366 (mt) cc_final: 0.8157 (mt) REVERT: D 375 MET cc_start: 0.8741 (tmm) cc_final: 0.8436 (tmm) REVERT: D 378 SER cc_start: 0.8681 (m) cc_final: 0.8451 (p) REVERT: D 434 MET cc_start: 0.7213 (mmt) cc_final: 0.6983 (mtt) REVERT: E 2 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7989 (mp0) REVERT: E 14 ARG cc_start: 0.8100 (ppp-140) cc_final: 0.7701 (ptm160) REVERT: E 87 GLU cc_start: 0.9134 (mp0) cc_final: 0.8639 (mp0) REVERT: E 148 ASP cc_start: 0.8778 (m-30) cc_final: 0.8531 (m-30) REVERT: E 201 GLU cc_start: 0.8357 (pp20) cc_final: 0.8049 (pp20) REVERT: E 231 MET cc_start: 0.7968 (pmm) cc_final: 0.7503 (tpt) REVERT: E 331 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8902 (mm) REVERT: E 338 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8624 (pm20) REVERT: E 383 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (t0) REVERT: E 408 LEU cc_start: 0.8886 (tt) cc_final: 0.8635 (tp) REVERT: E 460 LYS cc_start: 0.9041 (tttp) cc_final: 0.8788 (pttt) REVERT: E 469 ARG cc_start: 0.9132 (ttp80) cc_final: 0.8794 (ttp80) REVERT: E 473 ASN cc_start: 0.8696 (t0) cc_final: 0.8423 (t0) REVERT: E 485 GLN cc_start: 0.8759 (mt0) cc_final: 0.8245 (mp10) REVERT: E 637 ASN cc_start: 0.8441 (t0) cc_final: 0.8212 (t0) REVERT: E 674 ASN cc_start: 0.9134 (m-40) cc_final: 0.8809 (m-40) REVERT: E 687 ARG cc_start: 0.7954 (mpp-170) cc_final: 0.7747 (mpp-170) REVERT: E 698 GLN cc_start: 0.8058 (tt0) cc_final: 0.7693 (pt0) REVERT: E 809 TYR cc_start: 0.8644 (m-80) cc_final: 0.8133 (m-80) REVERT: F 380 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8733 (t-170) REVERT: F 490 ASP cc_start: 0.8325 (m-30) cc_final: 0.7755 (m-30) REVERT: F 517 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8680 (mp10) REVERT: F 527 HIS cc_start: 0.9035 (OUTLIER) cc_final: 0.8812 (m170) REVERT: F 528 LEU cc_start: 0.9194 (tp) cc_final: 0.8853 (tp) REVERT: F 533 ARG cc_start: 0.8598 (ptt90) cc_final: 0.8355 (ptt90) REVERT: F 615 LYS cc_start: 0.8671 (mttt) cc_final: 0.8248 (mtmm) REVERT: F 651 TYR cc_start: 0.9197 (t80) cc_final: 0.8918 (t80) REVERT: F 659 GLU cc_start: 0.8922 (tp30) cc_final: 0.8566 (mm-30) REVERT: F 663 GLU cc_start: 0.9108 (tp30) cc_final: 0.8849 (tp30) REVERT: F 680 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8185 (p0) REVERT: F 717 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8335 (tmmm) REVERT: F 726 SER cc_start: 0.9385 (t) cc_final: 0.9072 (p) REVERT: F 831 LYS cc_start: 0.8680 (tppt) cc_final: 0.8390 (tppt) REVERT: G 144 ARG cc_start: 0.8930 (mtp85) cc_final: 0.8660 (mmt-90) REVERT: G 161 ASP cc_start: 0.8846 (m-30) cc_final: 0.8529 (m-30) REVERT: G 172 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8439 (tp30) REVERT: G 342 ASN cc_start: 0.9013 (m-40) cc_final: 0.8348 (t0) REVERT: G 441 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8507 (mmmm) REVERT: G 450 TYR cc_start: 0.8050 (m-10) cc_final: 0.7566 (m-10) REVERT: G 469 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8728 (ttp80) REVERT: G 487 ASP cc_start: 0.8797 (t0) cc_final: 0.8497 (t0) REVERT: G 582 TYR cc_start: 0.9385 (m-10) cc_final: 0.9128 (m-80) REVERT: G 594 TYR cc_start: 0.9198 (t80) cc_final: 0.8652 (t80) REVERT: G 806 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8602 (ptp-170) REVERT: H 239 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8341 (tp30) REVERT: H 289 GLU cc_start: 0.8752 (tp30) cc_final: 0.8340 (tp30) REVERT: H 315 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8316 (mm-30) REVERT: H 420 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8420 (tm-30) REVERT: H 478 LYS cc_start: 0.8619 (ttpp) cc_final: 0.8366 (ttmt) REVERT: H 521 GLN cc_start: 0.9005 (mt0) cc_final: 0.8771 (pt0) REVERT: H 522 LEU cc_start: 0.9369 (mp) cc_final: 0.9103 (mt) REVERT: H 527 HIS cc_start: 0.7661 (m-70) cc_final: 0.7198 (m-70) REVERT: H 529 MET cc_start: 0.8709 (tmm) cc_final: 0.8330 (tmm) REVERT: H 592 ARG cc_start: 0.7843 (mtt-85) cc_final: 0.7208 (mtt180) REVERT: H 647 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8520 (tptt) REVERT: H 662 LYS cc_start: 0.9394 (tppp) cc_final: 0.8929 (tptp) REVERT: H 690 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7722 (pp20) REVERT: H 691 LEU cc_start: 0.8723 (tp) cc_final: 0.8376 (tm) REVERT: H 717 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8170 (tmmt) REVERT: H 725 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: H 835 ASP cc_start: 0.8714 (m-30) cc_final: 0.8350 (m-30) REVERT: H 836 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: H 844 SER cc_start: 0.9341 (t) cc_final: 0.8940 (p) REVERT: K 115 MET cc_start: 0.8106 (ptt) cc_final: 0.7769 (ptt) REVERT: K 122 GLN cc_start: 0.8488 (tp40) cc_final: 0.7904 (tm-30) REVERT: K 126 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8578 (mm-30) REVERT: K 130 LYS cc_start: 0.9396 (ttmt) cc_final: 0.9076 (tttp) REVERT: K 149 THR cc_start: 0.6698 (p) cc_final: 0.6416 (p) REVERT: Y 117 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7227 (pp30) REVERT: Y 125 ARG cc_start: 0.8677 (ttm110) cc_final: 0.8412 (ttm110) outliers start: 175 outliers final: 76 residues processed: 1028 average time/residue: 0.6433 time to fit residues: 823.2854 Evaluate side-chains 973 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 871 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 247 TYR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 437 TYR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 379 TYR Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain F residue 486 SER Chi-restraints excluded: chain F residue 527 HIS Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 643 GLN Chi-restraints excluded: chain F residue 647 LYS Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 696 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain F residue 717 LYS Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 469 ARG Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 806 ARG Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 277 VAL Chi-restraints excluded: chain H residue 339 ILE Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 404 MET Chi-restraints excluded: chain H residue 423 ASN Chi-restraints excluded: chain H residue 523 SER Chi-restraints excluded: chain H residue 539 ASN Chi-restraints excluded: chain H residue 647 LYS Chi-restraints excluded: chain H residue 681 LEU Chi-restraints excluded: chain H residue 690 GLU Chi-restraints excluded: chain H residue 717 LYS Chi-restraints excluded: chain H residue 725 GLU Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 784 TYR Chi-restraints excluded: chain H residue 836 GLU Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 GLN Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 316 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 320 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 390 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 325 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN E 222 ASN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 673 GLN ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.095040 restraints weight = 79822.701| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.52 r_work: 0.3164 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 40159 Z= 0.175 Angle : 0.672 16.276 54339 Z= 0.332 Chirality : 0.044 0.413 6052 Planarity : 0.004 0.062 6995 Dihedral : 7.756 178.879 5316 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.90 % Allowed : 23.39 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.12), residues: 4773 helix: 1.43 (0.10), residues: 2748 sheet: -1.01 (0.27), residues: 361 loop : -0.96 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 439 TYR 0.030 0.002 TYR F 816 PHE 0.029 0.002 PHE H 641 TRP 0.025 0.002 TRP D 105 HIS 0.009 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00399 (40155) covalent geometry : angle 0.67240 (54339) hydrogen bonds : bond 0.04460 ( 2274) hydrogen bonds : angle 4.56522 ( 6699) Misc. bond : bond 0.00049 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 932 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASN cc_start: 0.7630 (m110) cc_final: 0.7358 (m110) REVERT: B 36 LEU cc_start: 0.9153 (mm) cc_final: 0.8625 (pt) REVERT: B 47 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.6999 (t0) REVERT: B 84 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8305 (tpp80) REVERT: B 90 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8098 (ttp80) REVERT: B 125 LYS cc_start: 0.9326 (tttm) cc_final: 0.8870 (ttpp) REVERT: B 161 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8032 (tpm170) REVERT: B 169 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8480 (t) REVERT: B 173 PHE cc_start: 0.8542 (m-10) cc_final: 0.8305 (m-10) REVERT: B 215 LYS cc_start: 0.8670 (tppp) cc_final: 0.7843 (mttt) REVERT: B 287 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.6017 (tptt) REVERT: B 327 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7463 (tm-30) REVERT: B 347 TRP cc_start: 0.7138 (p-90) cc_final: 0.6369 (p-90) REVERT: B 375 MET cc_start: 0.8372 (tmm) cc_final: 0.8056 (tmm) REVERT: A 47 ASP cc_start: 0.8425 (p0) cc_final: 0.7891 (p0) REVERT: A 74 SER cc_start: 0.9307 (t) cc_final: 0.9074 (p) REVERT: A 88 ASP cc_start: 0.8020 (t0) cc_final: 0.7457 (t0) REVERT: A 90 ARG cc_start: 0.8662 (mtm110) cc_final: 0.8371 (mtm110) REVERT: A 93 TRP cc_start: 0.8274 (t60) cc_final: 0.8054 (t60) REVERT: A 125 LYS cc_start: 0.9410 (tppt) cc_final: 0.8985 (tppt) REVERT: A 156 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 161 ARG cc_start: 0.9346 (tpp80) cc_final: 0.9056 (ttm170) REVERT: A 167 LEU cc_start: 0.9444 (mm) cc_final: 0.9081 (mm) REVERT: A 272 PHE cc_start: 0.8916 (t80) cc_final: 0.8611 (t80) REVERT: A 300 ASP cc_start: 0.8958 (t70) cc_final: 0.8622 (t70) REVERT: A 422 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8230 (mm-30) REVERT: C 13 CYS cc_start: 0.9104 (t) cc_final: 0.8775 (t) REVERT: C 36 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8567 (mm) REVERT: C 47 ASP cc_start: 0.8978 (m-30) cc_final: 0.8591 (p0) REVERT: C 49 ASP cc_start: 0.8658 (t0) cc_final: 0.8425 (t0) REVERT: C 69 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: C 83 PHE cc_start: 0.8804 (m-80) cc_final: 0.8275 (m-80) REVERT: C 125 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9036 (mptt) REVERT: C 156 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8416 (mm-30) REVERT: C 187 THR cc_start: 0.9007 (m) cc_final: 0.8719 (p) REVERT: C 434 MET cc_start: 0.8762 (mtm) cc_final: 0.8387 (mtm) REVERT: D 16 HIS cc_start: 0.9084 (m170) cc_final: 0.8677 (m170) REVERT: D 27 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8746 (mmtm) REVERT: D 36 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8504 (mm) REVERT: D 110 ASP cc_start: 0.7805 (t0) cc_final: 0.7280 (t0) REVERT: D 138 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6801 (mp) REVERT: D 155 LEU cc_start: 0.9217 (mt) cc_final: 0.8965 (mt) REVERT: D 165 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8125 (mppt) REVERT: D 217 PHE cc_start: 0.8351 (m-80) cc_final: 0.7906 (m-80) REVERT: D 252 MET cc_start: 0.7727 (mmm) cc_final: 0.7320 (mmm) REVERT: D 308 THR cc_start: 0.6876 (p) cc_final: 0.6605 (p) REVERT: D 321 THR cc_start: 0.9014 (m) cc_final: 0.8588 (p) REVERT: D 434 MET cc_start: 0.7245 (mmt) cc_final: 0.6921 (mtt) REVERT: D 441 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7334 (mp0) REVERT: E 2 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8026 (mp0) REVERT: E 14 ARG cc_start: 0.8078 (ppp-140) cc_final: 0.7681 (ptm160) REVERT: E 148 ASP cc_start: 0.8790 (m-30) cc_final: 0.8535 (m-30) REVERT: E 201 GLU cc_start: 0.8352 (pp20) cc_final: 0.8063 (pp20) REVERT: E 222 ASN cc_start: -0.0246 (OUTLIER) cc_final: -0.0617 (p0) REVERT: E 231 MET cc_start: 0.8083 (pmm) cc_final: 0.7630 (tpt) REVERT: E 285 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8554 (mm-30) REVERT: E 331 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8904 (mm) REVERT: E 338 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: E 340 ASP cc_start: 0.8814 (m-30) cc_final: 0.8272 (m-30) REVERT: E 383 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8158 (t0) REVERT: E 408 LEU cc_start: 0.8920 (tt) cc_final: 0.8682 (tp) REVERT: E 460 LYS cc_start: 0.9053 (tttp) cc_final: 0.8720 (ptmt) REVERT: E 469 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8744 (ttp80) REVERT: E 473 ASN cc_start: 0.8718 (t0) cc_final: 0.8444 (t0) REVERT: E 485 GLN cc_start: 0.8717 (mt0) cc_final: 0.8185 (mp10) REVERT: E 487 ASP cc_start: 0.8817 (t0) cc_final: 0.8479 (p0) REVERT: E 614 TYR cc_start: 0.7828 (t80) cc_final: 0.7497 (t80) REVERT: E 624 ARG cc_start: 0.6684 (mtp85) cc_final: 0.6475 (ttt90) REVERT: E 674 ASN cc_start: 0.9143 (m-40) cc_final: 0.8820 (m-40) REVERT: E 684 MET cc_start: 0.8600 (mmm) cc_final: 0.7846 (tpp) REVERT: E 687 ARG cc_start: 0.7983 (mpp-170) cc_final: 0.7775 (mpp-170) REVERT: E 698 GLN cc_start: 0.8043 (tt0) cc_final: 0.7695 (pt0) REVERT: E 809 TYR cc_start: 0.8611 (m-80) cc_final: 0.8151 (m-80) REVERT: F 355 LEU cc_start: 0.9487 (mt) cc_final: 0.9156 (mt) REVERT: F 377 PHE cc_start: 0.9390 (m-80) cc_final: 0.9167 (m-80) REVERT: F 380 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8707 (t70) REVERT: F 517 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8832 (pt0) REVERT: F 527 HIS cc_start: 0.9019 (m170) cc_final: 0.8781 (m170) REVERT: F 528 LEU cc_start: 0.9203 (tp) cc_final: 0.8868 (tp) REVERT: F 615 LYS cc_start: 0.8676 (mttt) cc_final: 0.8264 (mtmm) REVERT: F 648 MET cc_start: 0.9306 (mmm) cc_final: 0.8956 (mmm) REVERT: F 651 TYR cc_start: 0.9146 (t80) cc_final: 0.8897 (t80) REVERT: F 659 GLU cc_start: 0.8964 (tp30) cc_final: 0.8620 (mm-30) REVERT: F 663 GLU cc_start: 0.9139 (tp30) cc_final: 0.8877 (tp30) REVERT: F 680 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8175 (p0) REVERT: F 689 ILE cc_start: 0.9110 (mt) cc_final: 0.8793 (mp) REVERT: F 717 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8305 (tmmm) REVERT: F 726 SER cc_start: 0.9374 (t) cc_final: 0.9056 (p) REVERT: F 790 MET cc_start: 0.6905 (mmp) cc_final: 0.6632 (ttm) REVERT: F 816 TYR cc_start: 0.8771 (t80) cc_final: 0.8539 (t80) REVERT: F 831 LYS cc_start: 0.8731 (tppt) cc_final: 0.8494 (tppt) REVERT: G 144 ARG cc_start: 0.8932 (mtp85) cc_final: 0.8501 (mmt-90) REVERT: G 156 GLU cc_start: 0.8337 (tp30) cc_final: 0.7984 (tm-30) REVERT: G 342 ASN cc_start: 0.9007 (m-40) cc_final: 0.8356 (t0) REVERT: G 450 TYR cc_start: 0.8008 (m-10) cc_final: 0.7566 (m-10) REVERT: G 468 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8856 (pt0) REVERT: G 469 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8661 (ttp80) REVERT: G 486 PHE cc_start: 0.7333 (t80) cc_final: 0.7023 (t80) REVERT: G 487 ASP cc_start: 0.8770 (t0) cc_final: 0.8482 (t0) REVERT: G 582 TYR cc_start: 0.9373 (m-10) cc_final: 0.9169 (m-80) REVERT: G 594 TYR cc_start: 0.9192 (t80) cc_final: 0.8650 (t80) REVERT: G 645 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8697 (tt0) REVERT: G 663 TYR cc_start: 0.8599 (p90) cc_final: 0.8392 (p90) REVERT: G 806 ARG cc_start: 0.8876 (ttp-170) cc_final: 0.8527 (ptp-170) REVERT: H 239 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: H 273 SER cc_start: 0.8871 (m) cc_final: 0.8541 (t) REVERT: H 289 GLU cc_start: 0.8755 (tp30) cc_final: 0.8372 (tp30) REVERT: H 315 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8332 (mm-30) REVERT: H 420 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8440 (tm-30) REVERT: H 521 GLN cc_start: 0.8990 (mt0) cc_final: 0.8786 (pt0) REVERT: H 527 HIS cc_start: 0.7614 (m-70) cc_final: 0.7053 (m-70) REVERT: H 529 MET cc_start: 0.8656 (tmm) cc_final: 0.8301 (tmm) REVERT: H 592 ARG cc_start: 0.7838 (mtt-85) cc_final: 0.7196 (mtm180) REVERT: H 647 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8563 (tptt) REVERT: H 662 LYS cc_start: 0.9384 (tppp) cc_final: 0.8925 (tptp) REVERT: H 690 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: H 691 LEU cc_start: 0.8730 (tp) cc_final: 0.8376 (tm) REVERT: H 717 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7877 (tmmt) REVERT: H 725 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8557 (tp30) REVERT: H 835 ASP cc_start: 0.8705 (m-30) cc_final: 0.8356 (m-30) REVERT: H 836 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: H 844 SER cc_start: 0.9331 (t) cc_final: 0.8925 (p) REVERT: K 115 MET cc_start: 0.8103 (ptt) cc_final: 0.7856 (ptt) REVERT: K 117 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: K 122 GLN cc_start: 0.8503 (tp40) cc_final: 0.7622 (tm-30) REVERT: K 126 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8434 (mm-30) REVERT: K 130 LYS cc_start: 0.9423 (ttmt) cc_final: 0.9083 (tttp) REVERT: K 132 GLU cc_start: 0.9068 (tp30) cc_final: 0.8377 (tm-30) REVERT: K 149 THR cc_start: 0.6802 (p) cc_final: 0.6509 (p) REVERT: Y 125 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8453 (ttm110) outliers start: 173 outliers final: 74 residues processed: 1021 average time/residue: 0.6358 time to fit residues: 812.2184 Evaluate side-chains 950 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 853 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 437 TYR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain E residue 663 TYR Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 379 TYR Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 643 GLN Chi-restraints excluded: chain F residue 647 LYS Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 696 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain F residue 717 LYS Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 469 ARG Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 711 LYS Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 277 VAL Chi-restraints excluded: chain H residue 339 ILE Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 404 MET Chi-restraints excluded: chain H residue 523 SER Chi-restraints excluded: chain H residue 539 ASN Chi-restraints excluded: chain H residue 647 LYS Chi-restraints excluded: chain H residue 681 LEU Chi-restraints excluded: chain H residue 690 GLU Chi-restraints excluded: chain H residue 717 LYS Chi-restraints excluded: chain H residue 725 GLU Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 836 GLU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 245 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 343 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 355 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 394 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 303 ASN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN E 222 ASN E 589 GLN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 ASN ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 122 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.095102 restraints weight = 80032.178| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.60 r_work: 0.3181 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 40159 Z= 0.152 Angle : 0.686 15.574 54339 Z= 0.337 Chirality : 0.044 0.423 6052 Planarity : 0.004 0.050 6995 Dihedral : 7.715 178.950 5316 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.67 % Allowed : 24.92 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 4773 helix: 1.50 (0.10), residues: 2750 sheet: -0.99 (0.27), residues: 356 loop : -0.89 (0.16), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 204 TYR 0.034 0.001 TYR G 725 PHE 0.031 0.002 PHE H 641 TRP 0.028 0.002 TRP D 105 HIS 0.013 0.001 HIS H 459 Details of bonding type rmsd covalent geometry : bond 0.00346 (40155) covalent geometry : angle 0.68576 (54339) hydrogen bonds : bond 0.04394 ( 2274) hydrogen bonds : angle 4.54905 ( 6699) Misc. bond : bond 0.00052 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 953 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 LEU cc_start: 0.9159 (mm) cc_final: 0.8635 (pt) REVERT: B 47 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7030 (t0) REVERT: B 69 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.6694 (ppp) REVERT: B 84 ARG cc_start: 0.8795 (mmm160) cc_final: 0.8287 (tpp80) REVERT: B 90 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8084 (ttp80) REVERT: B 125 LYS cc_start: 0.9341 (tttm) cc_final: 0.8863 (ttpp) REVERT: B 161 ARG cc_start: 0.8785 (mmm160) cc_final: 0.7724 (tpm170) REVERT: B 169 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8457 (t) REVERT: B 173 PHE cc_start: 0.8552 (m-10) cc_final: 0.8328 (m-10) REVERT: B 265 LEU cc_start: 0.8690 (mm) cc_final: 0.8442 (mm) REVERT: B 287 LYS cc_start: 0.6282 (OUTLIER) cc_final: 0.6009 (tptt) REVERT: B 347 TRP cc_start: 0.7001 (p-90) cc_final: 0.6318 (p-90) REVERT: A 47 ASP cc_start: 0.8464 (p0) cc_final: 0.7909 (p0) REVERT: A 55 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8421 (ttp80) REVERT: A 56 GLU cc_start: 0.8064 (tt0) cc_final: 0.7740 (tp30) REVERT: A 74 SER cc_start: 0.9310 (t) cc_final: 0.9063 (p) REVERT: A 88 ASP cc_start: 0.8026 (t0) cc_final: 0.7528 (t0) REVERT: A 90 ARG cc_start: 0.8684 (mtm110) cc_final: 0.8423 (mtm110) REVERT: A 125 LYS cc_start: 0.9351 (tppt) cc_final: 0.8965 (tppt) REVERT: A 156 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 167 LEU cc_start: 0.9423 (mm) cc_final: 0.9046 (mm) REVERT: A 300 ASP cc_start: 0.8931 (t70) cc_final: 0.8577 (t70) REVERT: A 422 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8211 (mm-30) REVERT: C 13 CYS cc_start: 0.9105 (t) cc_final: 0.8778 (t) REVERT: C 36 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8628 (mm) REVERT: C 47 ASP cc_start: 0.8953 (m-30) cc_final: 0.8606 (p0) REVERT: C 49 ASP cc_start: 0.8684 (t0) cc_final: 0.8445 (t0) REVERT: C 69 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7640 (mmm) REVERT: C 83 PHE cc_start: 0.8772 (m-80) cc_final: 0.8239 (m-80) REVERT: C 125 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9039 (mptt) REVERT: C 156 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 187 THR cc_start: 0.8978 (m) cc_final: 0.8671 (p) REVERT: C 275 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7380 (p90) REVERT: C 434 MET cc_start: 0.8738 (mtm) cc_final: 0.8271 (mtm) REVERT: D 16 HIS cc_start: 0.9101 (m170) cc_final: 0.8712 (m170) REVERT: D 36 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8540 (mm) REVERT: D 110 ASP cc_start: 0.7690 (t0) cc_final: 0.7170 (t0) REVERT: D 138 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6759 (mp) REVERT: D 155 LEU cc_start: 0.9222 (mt) cc_final: 0.8974 (mt) REVERT: D 165 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8127 (mppt) REVERT: D 217 PHE cc_start: 0.8382 (m-80) cc_final: 0.7932 (m-80) REVERT: D 252 MET cc_start: 0.7727 (mmm) cc_final: 0.7465 (mmm) REVERT: D 308 THR cc_start: 0.6909 (p) cc_final: 0.6572 (p) REVERT: D 321 THR cc_start: 0.9000 (m) cc_final: 0.8512 (p) REVERT: D 434 MET cc_start: 0.7321 (mmt) cc_final: 0.7033 (mtt) REVERT: D 441 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7407 (mp0) REVERT: E 2 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8023 (mp0) REVERT: E 14 ARG cc_start: 0.8065 (ppp-140) cc_final: 0.7674 (ptm160) REVERT: E 87 GLU cc_start: 0.9122 (mp0) cc_final: 0.8766 (pm20) REVERT: E 148 ASP cc_start: 0.8742 (m-30) cc_final: 0.8492 (m-30) REVERT: E 201 GLU cc_start: 0.8390 (pp20) cc_final: 0.8105 (pp20) REVERT: E 222 ASN cc_start: -0.0760 (OUTLIER) cc_final: -0.1320 (p0) REVERT: E 231 MET cc_start: 0.8004 (pmm) cc_final: 0.7607 (tpt) REVERT: E 338 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: E 340 ASP cc_start: 0.8837 (m-30) cc_final: 0.8312 (m-30) REVERT: E 383 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8148 (t0) REVERT: E 408 LEU cc_start: 0.8876 (tt) cc_final: 0.8645 (tp) REVERT: E 460 LYS cc_start: 0.9062 (tttp) cc_final: 0.8747 (ptmt) REVERT: E 469 ARG cc_start: 0.9161 (ttp80) cc_final: 0.8786 (ttp80) REVERT: E 473 ASN cc_start: 0.8704 (t0) cc_final: 0.8414 (t0) REVERT: E 484 ILE cc_start: 0.8640 (tp) cc_final: 0.8323 (mt) REVERT: E 485 GLN cc_start: 0.8720 (mt0) cc_final: 0.8079 (mp10) REVERT: E 486 PHE cc_start: 0.8756 (m-80) cc_final: 0.8465 (m-80) REVERT: E 487 ASP cc_start: 0.8841 (t0) cc_final: 0.8303 (p0) REVERT: E 614 TYR cc_start: 0.7884 (t80) cc_final: 0.7547 (t80) REVERT: E 637 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7816 (t0) REVERT: E 674 ASN cc_start: 0.9157 (m-40) cc_final: 0.8789 (m-40) REVERT: E 684 MET cc_start: 0.8627 (mmm) cc_final: 0.7968 (tpp) REVERT: E 698 GLN cc_start: 0.8004 (tt0) cc_final: 0.7726 (pt0) REVERT: E 809 TYR cc_start: 0.8565 (m-80) cc_final: 0.8165 (m-80) REVERT: F 242 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7891 (ttp80) REVERT: F 355 LEU cc_start: 0.9476 (mt) cc_final: 0.9140 (mt) REVERT: F 377 PHE cc_start: 0.9355 (m-80) cc_final: 0.9151 (m-80) REVERT: F 380 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.8714 (t-170) REVERT: F 527 HIS cc_start: 0.9013 (m170) cc_final: 0.8790 (m170) REVERT: F 528 LEU cc_start: 0.9156 (tp) cc_final: 0.8818 (tp) REVERT: F 533 ARG cc_start: 0.8607 (ptt90) cc_final: 0.8247 (ptt90) REVERT: F 615 LYS cc_start: 0.8635 (mttt) cc_final: 0.8234 (mtmm) REVERT: F 651 TYR cc_start: 0.9171 (t80) cc_final: 0.8945 (t80) REVERT: F 659 GLU cc_start: 0.8963 (tp30) cc_final: 0.8680 (mm-30) REVERT: F 663 GLU cc_start: 0.9134 (tp30) cc_final: 0.8844 (tp30) REVERT: F 680 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8106 (p0) REVERT: F 689 ILE cc_start: 0.9079 (mt) cc_final: 0.8813 (mp) REVERT: F 726 SER cc_start: 0.9363 (t) cc_final: 0.9052 (p) REVERT: F 790 MET cc_start: 0.7071 (mmp) cc_final: 0.6639 (ttm) REVERT: F 816 TYR cc_start: 0.8752 (t80) cc_final: 0.8540 (t80) REVERT: F 821 ASP cc_start: 0.8398 (m-30) cc_final: 0.7840 (p0) REVERT: G 144 ARG cc_start: 0.8930 (mtp85) cc_final: 0.8648 (mmt-90) REVERT: G 156 GLU cc_start: 0.8325 (tp30) cc_final: 0.8074 (tm-30) REVERT: G 342 ASN cc_start: 0.9003 (m-40) cc_final: 0.8326 (t0) REVERT: G 450 TYR cc_start: 0.7988 (m-10) cc_final: 0.7692 (m-10) REVERT: G 468 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8834 (pt0) REVERT: G 469 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8631 (ttp80) REVERT: G 487 ASP cc_start: 0.8765 (t0) cc_final: 0.8467 (t0) REVERT: G 594 TYR cc_start: 0.9189 (t80) cc_final: 0.8662 (t80) REVERT: G 645 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8684 (tt0) REVERT: G 709 PHE cc_start: 0.8947 (t80) cc_final: 0.8699 (t80) REVERT: G 806 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8555 (ptp-170) REVERT: H 226 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: H 239 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8270 (tp30) REVERT: H 273 SER cc_start: 0.8861 (m) cc_final: 0.8549 (t) REVERT: H 289 GLU cc_start: 0.8686 (tp30) cc_final: 0.8423 (tp30) REVERT: H 315 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8363 (mm-30) REVERT: H 420 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8403 (tm-30) REVERT: H 423 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8125 (t0) REVERT: H 509 ASN cc_start: 0.8370 (m110) cc_final: 0.8133 (m-40) REVERT: H 527 HIS cc_start: 0.7623 (m-70) cc_final: 0.7029 (m-70) REVERT: H 529 MET cc_start: 0.8668 (tmm) cc_final: 0.8264 (tmm) REVERT: H 592 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7194 (mtt180) REVERT: H 647 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8423 (tptt) REVERT: H 662 LYS cc_start: 0.9371 (tppp) cc_final: 0.8913 (tptp) REVERT: H 690 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: H 691 LEU cc_start: 0.8783 (tp) cc_final: 0.8457 (tm) REVERT: H 717 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7880 (tmmt) REVERT: H 725 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8567 (tp30) REVERT: H 836 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: H 844 SER cc_start: 0.9310 (t) cc_final: 0.8926 (p) REVERT: K 115 MET cc_start: 0.8112 (ptt) cc_final: 0.7850 (ptt) REVERT: K 116 SER cc_start: 0.9200 (t) cc_final: 0.8824 (t) REVERT: K 117 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: K 122 GLN cc_start: 0.8504 (tp40) cc_final: 0.7997 (tm-30) REVERT: K 130 LYS cc_start: 0.9417 (ttmt) cc_final: 0.9069 (tttp) REVERT: K 149 THR cc_start: 0.6885 (p) cc_final: 0.6602 (p) REVERT: Y 117 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7382 (pp30) REVERT: Y 133 ARG cc_start: 0.8867 (ttm-80) cc_final: 0.8460 (mpp80) outliers start: 163 outliers final: 82 residues processed: 1032 average time/residue: 0.6262 time to fit residues: 810.2791 Evaluate side-chains 998 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 889 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 437 TYR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 663 TYR Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 379 TYR Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 643 GLN Chi-restraints excluded: chain F residue 647 LYS Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 696 THR Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain F residue 780 ASN Chi-restraints excluded: chain G residue 123 TYR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 469 ARG Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 711 LYS Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 806 ARG Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 226 GLU Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 277 VAL Chi-restraints excluded: chain H residue 339 ILE Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 423 ASN Chi-restraints excluded: chain H residue 523 SER Chi-restraints excluded: chain H residue 539 ASN Chi-restraints excluded: chain H residue 541 LEU Chi-restraints excluded: chain H residue 647 LYS Chi-restraints excluded: chain H residue 681 LEU Chi-restraints excluded: chain H residue 690 GLU Chi-restraints excluded: chain H residue 717 LYS Chi-restraints excluded: chain H residue 725 GLU Chi-restraints excluded: chain H residue 736 LEU Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 836 GLU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 GLN Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 358 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 110 optimal weight: 0.0970 chunk 409 optimal weight: 0.6980 chunk 336 optimal weight: 4.9990 chunk 476 optimal weight: 6.9990 chunk 337 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 452 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 140 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN D 225 GLN D 303 ASN F 575 ASN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 521 GLN ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.137414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095760 restraints weight = 79980.360| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.62 r_work: 0.3186 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 40159 Z= 0.157 Angle : 0.714 15.645 54339 Z= 0.349 Chirality : 0.044 0.390 6052 Planarity : 0.004 0.052 6995 Dihedral : 7.697 179.587 5316 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 3.52 % Allowed : 26.25 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4773 helix: 1.54 (0.10), residues: 2744 sheet: -0.94 (0.28), residues: 336 loop : -0.83 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 776 TYR 0.029 0.001 TYR C 185 PHE 0.045 0.002 PHE H 641 TRP 0.031 0.002 TRP B 105 HIS 0.007 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00361 (40155) covalent geometry : angle 0.71397 (54339) hydrogen bonds : bond 0.04400 ( 2274) hydrogen bonds : angle 4.55741 ( 6699) Misc. bond : bond 0.00047 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 923 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASN cc_start: 0.7774 (m110) cc_final: 0.7199 (m110) REVERT: B 36 LEU cc_start: 0.9163 (mm) cc_final: 0.8651 (pt) REVERT: B 47 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7071 (t0) REVERT: B 69 MET cc_start: 0.7581 (ptt) cc_final: 0.6767 (ppp) REVERT: B 84 ARG cc_start: 0.8831 (mmm160) cc_final: 0.8290 (tpp80) REVERT: B 90 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8088 (ttp80) REVERT: B 103 ASN cc_start: 0.7794 (m-40) cc_final: 0.7238 (t0) REVERT: B 125 LYS cc_start: 0.9343 (tttm) cc_final: 0.8894 (ttpp) REVERT: B 161 ARG cc_start: 0.8787 (mmm160) cc_final: 0.7716 (tpm170) REVERT: B 169 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8399 (t) REVERT: B 170 TYR cc_start: 0.8785 (m-80) cc_final: 0.8543 (m-80) REVERT: B 173 PHE cc_start: 0.8468 (m-10) cc_final: 0.8247 (m-10) REVERT: B 196 GLU cc_start: 0.7851 (tp30) cc_final: 0.7474 (pt0) REVERT: B 265 LEU cc_start: 0.8727 (mm) cc_final: 0.8273 (mm) REVERT: B 287 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5947 (tptt) REVERT: B 327 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 347 TRP cc_start: 0.6983 (p-90) cc_final: 0.6306 (p-90) REVERT: B 414 GLN cc_start: 0.8760 (tt0) cc_final: 0.8104 (tm130) REVERT: A 47 ASP cc_start: 0.8493 (p0) cc_final: 0.7956 (p0) REVERT: A 74 SER cc_start: 0.9302 (t) cc_final: 0.9049 (p) REVERT: A 88 ASP cc_start: 0.8036 (t0) cc_final: 0.7507 (t0) REVERT: A 90 ARG cc_start: 0.8689 (mtm110) cc_final: 0.8428 (mtm110) REVERT: A 93 TRP cc_start: 0.8153 (t60) cc_final: 0.7851 (t60) REVERT: A 156 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8372 (mm-30) REVERT: A 167 LEU cc_start: 0.9393 (mm) cc_final: 0.8977 (mm) REVERT: A 300 ASP cc_start: 0.8935 (t70) cc_final: 0.8586 (t70) REVERT: A 422 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8207 (mm-30) REVERT: C 13 CYS cc_start: 0.9108 (t) cc_final: 0.8767 (t) REVERT: C 36 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8639 (mm) REVERT: C 47 ASP cc_start: 0.8967 (m-30) cc_final: 0.8557 (p0) REVERT: C 49 ASP cc_start: 0.8678 (t0) cc_final: 0.8444 (t0) REVERT: C 69 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7612 (mmm) REVERT: C 93 TRP cc_start: 0.8428 (t60) cc_final: 0.8089 (t60) REVERT: C 121 ASN cc_start: 0.9036 (m-40) cc_final: 0.8444 (m-40) REVERT: C 124 ASP cc_start: 0.8914 (t0) cc_final: 0.8674 (t0) REVERT: C 125 LYS cc_start: 0.9447 (mmmt) cc_final: 0.8945 (mmtp) REVERT: C 156 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8447 (mm-30) REVERT: C 165 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8329 (mmmm) REVERT: C 185 TYR cc_start: 0.9020 (m-80) cc_final: 0.8714 (m-80) REVERT: C 187 THR cc_start: 0.8959 (m) cc_final: 0.8684 (p) REVERT: C 275 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7362 (p90) REVERT: C 434 MET cc_start: 0.8688 (mtm) cc_final: 0.8175 (mtm) REVERT: D 16 HIS cc_start: 0.9083 (m170) cc_final: 0.8682 (m170) REVERT: D 36 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8483 (mm) REVERT: D 110 ASP cc_start: 0.7805 (t0) cc_final: 0.7268 (t0) REVERT: D 138 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6766 (mp) REVERT: D 155 LEU cc_start: 0.9220 (mt) cc_final: 0.8976 (mt) REVERT: D 165 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8342 (mmmm) REVERT: D 217 PHE cc_start: 0.8364 (m-80) cc_final: 0.8033 (m-80) REVERT: D 300 ASP cc_start: 0.8069 (t0) cc_final: 0.7646 (t0) REVERT: D 303 ASN cc_start: 0.7071 (OUTLIER) cc_final: 0.6830 (m-40) REVERT: D 308 THR cc_start: 0.6966 (p) cc_final: 0.6639 (p) REVERT: D 311 ASN cc_start: 0.7840 (p0) cc_final: 0.6569 (t0) REVERT: D 321 THR cc_start: 0.9017 (m) cc_final: 0.8508 (p) REVERT: D 352 MET cc_start: 0.8459 (pmm) cc_final: 0.8070 (ppp) REVERT: D 375 MET cc_start: 0.8602 (tmm) cc_final: 0.8310 (tmm) REVERT: D 434 MET cc_start: 0.7351 (mmt) cc_final: 0.7030 (mtt) REVERT: D 441 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7368 (mp0) REVERT: E 2 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8041 (mp0) REVERT: E 14 ARG cc_start: 0.8064 (ppp-140) cc_final: 0.7731 (tmm-80) REVERT: E 87 GLU cc_start: 0.9130 (mp0) cc_final: 0.8733 (pm20) REVERT: E 148 ASP cc_start: 0.8665 (m-30) cc_final: 0.8421 (m-30) REVERT: E 201 GLU cc_start: 0.8441 (pp20) cc_final: 0.8176 (pp20) REVERT: E 285 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8575 (mm-30) REVERT: E 338 GLU cc_start: 0.8869 (tt0) cc_final: 0.8641 (pm20) REVERT: E 340 ASP cc_start: 0.8815 (m-30) cc_final: 0.8350 (m-30) REVERT: E 383 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8117 (t0) REVERT: E 408 LEU cc_start: 0.8859 (tt) cc_final: 0.8629 (tp) REVERT: E 469 ARG cc_start: 0.9169 (ttp80) cc_final: 0.8843 (ttp80) REVERT: E 473 ASN cc_start: 0.8724 (t0) cc_final: 0.8428 (t0) REVERT: E 482 LEU cc_start: 0.9158 (tp) cc_final: 0.8881 (tm) REVERT: E 484 ILE cc_start: 0.8602 (tp) cc_final: 0.8367 (tp) REVERT: E 485 GLN cc_start: 0.8744 (mt0) cc_final: 0.8226 (mp10) REVERT: E 486 PHE cc_start: 0.8819 (m-80) cc_final: 0.8440 (m-80) REVERT: E 487 ASP cc_start: 0.8816 (t0) cc_final: 0.8293 (p0) REVERT: E 614 TYR cc_start: 0.7926 (t80) cc_final: 0.7577 (t80) REVERT: E 624 ARG cc_start: 0.6910 (mtp85) cc_final: 0.6708 (ttt90) REVERT: E 674 ASN cc_start: 0.9151 (m-40) cc_final: 0.8789 (m-40) REVERT: E 684 MET cc_start: 0.8632 (mmm) cc_final: 0.7976 (tpp) REVERT: E 687 ARG cc_start: 0.7905 (mpp-170) cc_final: 0.7693 (mmp-170) REVERT: E 698 GLN cc_start: 0.7974 (tt0) cc_final: 0.7699 (pt0) REVERT: E 809 TYR cc_start: 0.8570 (m-80) cc_final: 0.8173 (m-80) REVERT: F 355 LEU cc_start: 0.9477 (mt) cc_final: 0.9139 (mt) REVERT: F 377 PHE cc_start: 0.9299 (m-80) cc_final: 0.9081 (m-80) REVERT: F 380 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8693 (t-170) REVERT: F 517 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8754 (mt0) REVERT: F 527 HIS cc_start: 0.8984 (m170) cc_final: 0.8758 (m170) REVERT: F 528 LEU cc_start: 0.9144 (tp) cc_final: 0.8818 (tp) REVERT: F 615 LYS cc_start: 0.8633 (mttt) cc_final: 0.8225 (mtmm) REVERT: F 651 TYR cc_start: 0.9168 (t80) cc_final: 0.8944 (t80) REVERT: F 659 GLU cc_start: 0.8959 (tp30) cc_final: 0.8631 (mm-30) REVERT: F 663 GLU cc_start: 0.9143 (tp30) cc_final: 0.8820 (tp30) REVERT: F 666 ARG cc_start: 0.9166 (ttm-80) cc_final: 0.8938 (ttm-80) REVERT: F 689 ILE cc_start: 0.9034 (mt) cc_final: 0.8812 (mp) REVERT: F 717 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8139 (tmmm) REVERT: F 726 SER cc_start: 0.9354 (t) cc_final: 0.9067 (p) REVERT: F 790 MET cc_start: 0.6940 (mmp) cc_final: 0.6606 (ttm) REVERT: F 816 TYR cc_start: 0.8725 (t80) cc_final: 0.8512 (t80) REVERT: F 821 ASP cc_start: 0.8452 (m-30) cc_final: 0.7934 (p0) REVERT: F 835 ASP cc_start: 0.8797 (m-30) cc_final: 0.8311 (t70) REVERT: G 50 ASP cc_start: 0.9365 (m-30) cc_final: 0.9053 (p0) REVERT: G 144 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8642 (mmt-90) REVERT: G 156 GLU cc_start: 0.8344 (tp30) cc_final: 0.8034 (tm-30) REVERT: G 342 ASN cc_start: 0.8980 (m-40) cc_final: 0.8328 (t0) REVERT: G 450 TYR cc_start: 0.7974 (m-10) cc_final: 0.7627 (m-10) REVERT: G 468 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8894 (pt0) REVERT: G 469 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8614 (ttp80) REVERT: G 486 PHE cc_start: 0.7305 (t80) cc_final: 0.7002 (t80) REVERT: G 487 ASP cc_start: 0.8786 (t0) cc_final: 0.8499 (t0) REVERT: G 594 TYR cc_start: 0.9189 (t80) cc_final: 0.8755 (t80) REVERT: G 645 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8650 (tt0) REVERT: G 692 LEU cc_start: 0.9402 (mt) cc_final: 0.9193 (mm) REVERT: G 709 PHE cc_start: 0.8886 (t80) cc_final: 0.8616 (t80) REVERT: G 719 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7762 (mm110) REVERT: G 784 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8719 (tp-100) REVERT: G 806 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8571 (ptp-170) REVERT: H 226 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: H 239 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8283 (tp30) REVERT: H 273 SER cc_start: 0.8819 (m) cc_final: 0.8540 (t) REVERT: H 289 GLU cc_start: 0.8737 (tp30) cc_final: 0.8427 (tp30) REVERT: H 306 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: H 315 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8235 (mm-30) REVERT: H 420 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8417 (tm-30) REVERT: H 423 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8052 (t0) REVERT: H 509 ASN cc_start: 0.8325 (m110) cc_final: 0.8069 (m-40) REVERT: H 527 HIS cc_start: 0.7653 (m-70) cc_final: 0.7067 (m-70) REVERT: H 529 MET cc_start: 0.8659 (tmm) cc_final: 0.8340 (tmm) REVERT: H 592 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7189 (mtt180) REVERT: H 647 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8465 (tptt) REVERT: H 662 LYS cc_start: 0.9370 (tppp) cc_final: 0.8930 (tptp) REVERT: H 690 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7664 (pp20) REVERT: H 691 LEU cc_start: 0.8779 (tp) cc_final: 0.8454 (tm) REVERT: H 717 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7874 (tmmt) REVERT: H 725 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8681 (tp30) REVERT: H 790 MET cc_start: 0.7015 (tmm) cc_final: 0.6202 (mpt) REVERT: H 836 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8439 (tm-30) REVERT: H 837 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8426 (mm-30) REVERT: H 844 SER cc_start: 0.9298 (t) cc_final: 0.8930 (p) REVERT: K 116 SER cc_start: 0.9215 (t) cc_final: 0.8824 (t) REVERT: K 117 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: K 122 GLN cc_start: 0.8507 (tp40) cc_final: 0.7524 (tm-30) REVERT: K 126 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8440 (mm-30) REVERT: K 130 LYS cc_start: 0.9420 (ttmt) cc_final: 0.9067 (tttp) REVERT: K 149 THR cc_start: 0.6956 (p) cc_final: 0.6671 (p) REVERT: Y 117 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7422 (pp30) outliers start: 156 outliers final: 81 residues processed: 998 average time/residue: 0.6277 time to fit residues: 783.6070 Evaluate side-chains 977 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 869 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 437 TYR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain E residue 663 TYR Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 379 TYR Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 647 LYS Chi-restraints excluded: chain F residue 696 THR Chi-restraints excluded: chain F residue 717 LYS Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 469 ARG Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 711 LYS Chi-restraints excluded: chain G residue 719 GLN Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 784 GLN Chi-restraints excluded: chain G residue 806 ARG Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 226 GLU Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 277 VAL Chi-restraints excluded: chain H residue 306 GLU Chi-restraints excluded: chain H residue 339 ILE Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 423 ASN Chi-restraints excluded: chain H residue 500 LEU Chi-restraints excluded: chain H residue 523 SER Chi-restraints excluded: chain H residue 539 ASN Chi-restraints excluded: chain H residue 647 LYS Chi-restraints excluded: chain H residue 681 LEU Chi-restraints excluded: chain H residue 690 GLU Chi-restraints excluded: chain H residue 717 LYS Chi-restraints excluded: chain H residue 725 GLU Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 836 GLU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 GLN Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 chunk 464 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 237 optimal weight: 0.6980 chunk 334 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN A 132 ASN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN E 222 ASN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 GLN E 589 GLN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.136905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094899 restraints weight = 80921.287| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.70 r_work: 0.3197 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 40159 Z= 0.182 Angle : 0.746 15.375 54339 Z= 0.366 Chirality : 0.045 0.434 6052 Planarity : 0.004 0.055 6995 Dihedral : 7.694 179.450 5316 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 3.27 % Allowed : 26.81 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.12), residues: 4773 helix: 1.54 (0.10), residues: 2743 sheet: -0.92 (0.28), residues: 325 loop : -0.82 (0.16), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 204 TYR 0.027 0.002 TYR A 292 PHE 0.039 0.002 PHE H 641 TRP 0.033 0.002 TRP B 105 HIS 0.008 0.001 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00426 (40155) covalent geometry : angle 0.74606 (54339) hydrogen bonds : bond 0.04445 ( 2274) hydrogen bonds : angle 4.59606 ( 6699) Misc. bond : bond 0.00043 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 906 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASN cc_start: 0.7743 (m110) cc_final: 0.7449 (m110) REVERT: B 36 LEU cc_start: 0.9172 (mm) cc_final: 0.8630 (pt) REVERT: B 47 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.6974 (t0) REVERT: B 84 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8333 (tpp80) REVERT: B 90 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8069 (ttp80) REVERT: B 103 ASN cc_start: 0.7689 (m-40) cc_final: 0.7130 (t0) REVERT: B 125 LYS cc_start: 0.9321 (tttm) cc_final: 0.8874 (ttpp) REVERT: B 161 ARG cc_start: 0.8781 (mmm160) cc_final: 0.7723 (tpm170) REVERT: B 169 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8294 (t) REVERT: B 173 PHE cc_start: 0.8467 (m-10) cc_final: 0.8232 (m-10) REVERT: B 196 GLU cc_start: 0.7811 (tp30) cc_final: 0.7451 (pt0) REVERT: B 265 LEU cc_start: 0.8674 (mm) cc_final: 0.8166 (mm) REVERT: B 287 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5822 (tptt) REVERT: B 327 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 347 TRP cc_start: 0.6929 (p-90) cc_final: 0.6307 (p-90) REVERT: A 47 ASP cc_start: 0.8461 (p0) cc_final: 0.7876 (p0) REVERT: A 56 GLU cc_start: 0.8136 (tt0) cc_final: 0.7771 (tp30) REVERT: A 74 SER cc_start: 0.9290 (t) cc_final: 0.9052 (p) REVERT: A 88 ASP cc_start: 0.8098 (t0) cc_final: 0.7576 (t0) REVERT: A 90 ARG cc_start: 0.8692 (mtm110) cc_final: 0.8418 (mtm110) REVERT: A 93 TRP cc_start: 0.8166 (t60) cc_final: 0.7896 (t60) REVERT: A 125 LYS cc_start: 0.9282 (tppt) cc_final: 0.8894 (tppt) REVERT: A 132 ASN cc_start: 0.8932 (t0) cc_final: 0.8698 (t0) REVERT: A 156 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 167 LEU cc_start: 0.9335 (mm) cc_final: 0.8905 (mm) REVERT: A 300 ASP cc_start: 0.8968 (t70) cc_final: 0.8625 (t70) REVERT: A 363 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8742 (mm) REVERT: A 422 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8199 (mm-30) REVERT: C 13 CYS cc_start: 0.9126 (t) cc_final: 0.8760 (t) REVERT: C 36 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8606 (mm) REVERT: C 47 ASP cc_start: 0.8942 (m-30) cc_final: 0.8497 (p0) REVERT: C 49 ASP cc_start: 0.8649 (t0) cc_final: 0.8410 (t0) REVERT: C 69 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7556 (mmm) REVERT: C 93 TRP cc_start: 0.8450 (t60) cc_final: 0.8045 (t60) REVERT: C 121 ASN cc_start: 0.9036 (m-40) cc_final: 0.8555 (m-40) REVERT: C 125 LYS cc_start: 0.9446 (mmmt) cc_final: 0.8991 (mptt) REVERT: C 156 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8507 (mm-30) REVERT: C 187 THR cc_start: 0.8912 (m) cc_final: 0.8646 (p) REVERT: C 275 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7305 (p90) REVERT: C 434 MET cc_start: 0.8673 (mtm) cc_final: 0.8367 (mtm) REVERT: D 16 HIS cc_start: 0.9049 (m170) cc_final: 0.8618 (m170) REVERT: D 36 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8462 (mm) REVERT: D 110 ASP cc_start: 0.7852 (t0) cc_final: 0.7341 (t0) REVERT: D 138 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6651 (mp) REVERT: D 155 LEU cc_start: 0.9213 (mt) cc_final: 0.8964 (mt) REVERT: D 165 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8072 (mppt) REVERT: D 297 ASP cc_start: 0.8151 (p0) cc_final: 0.7914 (p0) REVERT: D 308 THR cc_start: 0.6929 (p) cc_final: 0.6633 (p) REVERT: D 311 ASN cc_start: 0.7780 (p0) cc_final: 0.6521 (t0) REVERT: D 321 THR cc_start: 0.9022 (m) cc_final: 0.8548 (p) REVERT: D 340 GLN cc_start: 0.8620 (pt0) cc_final: 0.8401 (pm20) REVERT: D 375 MET cc_start: 0.8531 (tmm) cc_final: 0.8163 (tmm) REVERT: D 376 MET cc_start: 0.8741 (ttt) cc_final: 0.8182 (tmm) REVERT: D 434 MET cc_start: 0.7443 (mmt) cc_final: 0.7088 (mtt) REVERT: E 2 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7921 (mp0) REVERT: E 87 GLU cc_start: 0.9151 (mp0) cc_final: 0.8718 (pm20) REVERT: E 148 ASP cc_start: 0.8659 (m-30) cc_final: 0.8385 (m-30) REVERT: E 201 GLU cc_start: 0.8491 (pp20) cc_final: 0.8278 (pp20) REVERT: E 231 MET cc_start: 0.7487 (pmm) cc_final: 0.7196 (tpt) REVERT: E 285 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8502 (mm-30) REVERT: E 338 GLU cc_start: 0.8866 (tt0) cc_final: 0.8612 (pm20) REVERT: E 383 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8065 (t0) REVERT: E 408 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (tp) REVERT: E 460 LYS cc_start: 0.9446 (pttt) cc_final: 0.9245 (pptt) REVERT: E 470 GLN cc_start: 0.9431 (mt0) cc_final: 0.8874 (mm110) REVERT: E 473 ASN cc_start: 0.8654 (t0) cc_final: 0.8353 (t0) REVERT: E 482 LEU cc_start: 0.9105 (tp) cc_final: 0.8887 (tm) REVERT: E 485 GLN cc_start: 0.8704 (mt0) cc_final: 0.8186 (mp10) REVERT: E 486 PHE cc_start: 0.8819 (m-80) cc_final: 0.8414 (m-80) REVERT: E 487 ASP cc_start: 0.8833 (t0) cc_final: 0.8252 (p0) REVERT: E 489 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: E 614 TYR cc_start: 0.7929 (t80) cc_final: 0.7570 (t80) REVERT: E 624 ARG cc_start: 0.6777 (mtp85) cc_final: 0.6576 (ttt90) REVERT: E 684 MET cc_start: 0.8552 (mmm) cc_final: 0.7887 (tpp) REVERT: E 687 ARG cc_start: 0.7944 (mpp-170) cc_final: 0.7734 (mmp-170) REVERT: E 698 GLN cc_start: 0.7992 (tt0) cc_final: 0.7694 (pt0) REVERT: E 809 TYR cc_start: 0.8592 (m-80) cc_final: 0.8167 (m-80) REVERT: F 242 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7837 (ttp80) REVERT: F 355 LEU cc_start: 0.9507 (mt) cc_final: 0.9265 (mt) REVERT: F 377 PHE cc_start: 0.9223 (m-80) cc_final: 0.8983 (m-80) REVERT: F 527 HIS cc_start: 0.8998 (m170) cc_final: 0.8767 (m170) REVERT: F 528 LEU cc_start: 0.9127 (tp) cc_final: 0.8797 (tp) REVERT: F 615 LYS cc_start: 0.8622 (mttt) cc_final: 0.8257 (mtmm) REVERT: F 651 TYR cc_start: 0.9209 (t80) cc_final: 0.8953 (t80) REVERT: F 659 GLU cc_start: 0.9039 (tp30) cc_final: 0.8733 (mm-30) REVERT: F 663 GLU cc_start: 0.9195 (tp30) cc_final: 0.8736 (tp30) REVERT: F 666 ARG cc_start: 0.9197 (ttm-80) cc_final: 0.8746 (mtm110) REVERT: F 689 ILE cc_start: 0.8993 (mt) cc_final: 0.8749 (mp) REVERT: F 717 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8133 (tmmm) REVERT: F 726 SER cc_start: 0.9340 (t) cc_final: 0.9046 (p) REVERT: F 821 ASP cc_start: 0.8474 (m-30) cc_final: 0.7950 (p0) REVERT: G 144 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8603 (mmt-90) REVERT: G 156 GLU cc_start: 0.8306 (tp30) cc_final: 0.7940 (tm-30) REVERT: G 342 ASN cc_start: 0.8923 (m-40) cc_final: 0.8264 (t0) REVERT: G 450 TYR cc_start: 0.7929 (m-10) cc_final: 0.7625 (m-10) REVERT: G 468 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8914 (pt0) REVERT: G 469 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8693 (ttp80) REVERT: G 486 PHE cc_start: 0.7185 (t80) cc_final: 0.6906 (t80) REVERT: G 487 ASP cc_start: 0.8752 (t0) cc_final: 0.8441 (t0) REVERT: G 594 TYR cc_start: 0.9237 (t80) cc_final: 0.8830 (t80) REVERT: G 604 MET cc_start: 0.9096 (tpt) cc_final: 0.8812 (mmm) REVERT: G 645 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8792 (tt0) REVERT: G 661 LYS cc_start: 0.9409 (pptt) cc_final: 0.9194 (ptpp) REVERT: G 692 LEU cc_start: 0.9360 (mt) cc_final: 0.9123 (mm) REVERT: G 709 PHE cc_start: 0.8909 (t80) cc_final: 0.8603 (t80) REVERT: G 719 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7726 (mm110) REVERT: G 784 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8754 (tp-100) REVERT: G 806 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8524 (ptp-170) REVERT: H 226 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: H 239 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: H 273 SER cc_start: 0.8813 (m) cc_final: 0.8540 (t) REVERT: H 289 GLU cc_start: 0.8877 (tp30) cc_final: 0.8575 (tp30) REVERT: H 306 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: H 315 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8269 (mm-30) REVERT: H 420 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8434 (tm-30) REVERT: H 423 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.8029 (t0) REVERT: H 509 ASN cc_start: 0.8287 (m110) cc_final: 0.8018 (m-40) REVERT: H 527 HIS cc_start: 0.7596 (m-70) cc_final: 0.6961 (m-70) REVERT: H 529 MET cc_start: 0.8597 (tmm) cc_final: 0.8190 (tmm) REVERT: H 592 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7166 (mtt180) REVERT: H 647 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8388 (tptt) REVERT: H 662 LYS cc_start: 0.9307 (tppp) cc_final: 0.8843 (tptp) REVERT: H 690 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: H 717 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7906 (tmmt) REVERT: H 725 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8618 (tp30) REVERT: H 784 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: H 790 MET cc_start: 0.6977 (tmm) cc_final: 0.6243 (mpt) REVERT: H 836 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: H 844 SER cc_start: 0.9268 (t) cc_final: 0.8879 (p) REVERT: K 122 GLN cc_start: 0.8471 (tp40) cc_final: 0.7616 (tm-30) REVERT: K 126 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8413 (mm-30) REVERT: K 130 LYS cc_start: 0.9394 (ttmt) cc_final: 0.9024 (tttp) REVERT: K 132 GLU cc_start: 0.9048 (tp30) cc_final: 0.8320 (tm-30) REVERT: K 149 THR cc_start: 0.6790 (p) cc_final: 0.6518 (p) REVERT: Y 117 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7374 (pp30) REVERT: Y 136 ARG cc_start: 0.8724 (ttm110) cc_final: 0.8103 (ptp-110) outliers start: 145 outliers final: 86 residues processed: 980 average time/residue: 0.6176 time to fit residues: 756.9933 Evaluate side-chains 974 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 861 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 437 TYR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain E residue 663 TYR Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 379 TYR Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 643 GLN Chi-restraints excluded: chain F residue 647 LYS Chi-restraints excluded: chain F residue 696 THR Chi-restraints excluded: chain F residue 717 LYS Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain G residue 123 TYR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain G residue 392 LEU Chi-restraints excluded: chain G residue 469 ARG Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 711 LYS Chi-restraints excluded: chain G residue 719 GLN Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 784 GLN Chi-restraints excluded: chain G residue 806 ARG Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 226 GLU Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 277 VAL Chi-restraints excluded: chain H residue 306 GLU Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 423 ASN Chi-restraints excluded: chain H residue 500 LEU Chi-restraints excluded: chain H residue 523 SER Chi-restraints excluded: chain H residue 681 LEU Chi-restraints excluded: chain H residue 690 GLU Chi-restraints excluded: chain H residue 717 LYS Chi-restraints excluded: chain H residue 725 GLU Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 784 TYR Chi-restraints excluded: chain H residue 836 GLU Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 GLN Chi-restraints excluded: chain Y residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 167 optimal weight: 10.0000 chunk 162 optimal weight: 0.0010 chunk 373 optimal weight: 4.9990 chunk 339 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 429 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 97 optimal weight: 0.0010 chunk 307 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 320 optimal weight: 0.7980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN E 222 ASN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.138917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097430 restraints weight = 80249.895| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.64 r_work: 0.3228 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 40159 Z= 0.148 Angle : 0.770 15.548 54339 Z= 0.376 Chirality : 0.045 0.486 6052 Planarity : 0.004 0.056 6995 Dihedral : 7.660 179.025 5316 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.19 % Favored : 95.79 % Rotamer: Outliers : 2.66 % Allowed : 27.87 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.12), residues: 4773 helix: 1.55 (0.10), residues: 2747 sheet: -0.81 (0.28), residues: 329 loop : -0.72 (0.16), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 133 TYR 0.046 0.002 TYR F 816 PHE 0.049 0.002 PHE H 641 TRP 0.037 0.002 TRP D 105 HIS 0.007 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00342 (40155) covalent geometry : angle 0.77016 (54339) hydrogen bonds : bond 0.04359 ( 2274) hydrogen bonds : angle 4.60759 ( 6699) Misc. bond : bond 0.00047 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9546 Ramachandran restraints generated. 4773 Oldfield, 0 Emsley, 4773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 963 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASN cc_start: 0.7769 (m110) cc_final: 0.7201 (m110) REVERT: B 36 LEU cc_start: 0.9177 (mm) cc_final: 0.8633 (pt) REVERT: B 47 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7014 (t0) REVERT: B 84 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8351 (tpp80) REVERT: B 90 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8091 (ttp80) REVERT: B 103 ASN cc_start: 0.7533 (m-40) cc_final: 0.6892 (t0) REVERT: B 125 LYS cc_start: 0.9346 (tttm) cc_final: 0.8908 (ttpp) REVERT: B 161 ARG cc_start: 0.8835 (mmm160) cc_final: 0.7944 (tpm170) REVERT: B 169 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8062 (t) REVERT: B 265 LEU cc_start: 0.8661 (mm) cc_final: 0.8161 (mm) REVERT: B 287 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5832 (tptt) REVERT: B 327 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 347 TRP cc_start: 0.6740 (p-90) cc_final: 0.6244 (p-90) REVERT: A 47 ASP cc_start: 0.8434 (p0) cc_final: 0.7881 (p0) REVERT: A 56 GLU cc_start: 0.8118 (tt0) cc_final: 0.7766 (tp30) REVERT: A 74 SER cc_start: 0.9280 (t) cc_final: 0.9031 (p) REVERT: A 88 ASP cc_start: 0.8057 (t0) cc_final: 0.7507 (t0) REVERT: A 90 ARG cc_start: 0.8699 (mtm110) cc_final: 0.8428 (mtm110) REVERT: A 93 TRP cc_start: 0.8132 (t60) cc_final: 0.7910 (t60) REVERT: A 156 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8434 (mm-30) REVERT: A 161 ARG cc_start: 0.9324 (ttm170) cc_final: 0.8938 (ttm170) REVERT: A 167 LEU cc_start: 0.9331 (mm) cc_final: 0.8882 (mm) REVERT: A 300 ASP cc_start: 0.8940 (t70) cc_final: 0.8562 (t0) REVERT: A 312 ASN cc_start: 0.8913 (m110) cc_final: 0.8612 (p0) REVERT: A 363 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8705 (mm) REVERT: A 422 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8188 (mm-30) REVERT: C 13 CYS cc_start: 0.9130 (t) cc_final: 0.8766 (t) REVERT: C 36 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8613 (mm) REVERT: C 47 ASP cc_start: 0.8897 (m-30) cc_final: 0.8487 (p0) REVERT: C 49 ASP cc_start: 0.8634 (t0) cc_final: 0.8422 (t0) REVERT: C 69 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7696 (mmm) REVERT: C 93 TRP cc_start: 0.8501 (t60) cc_final: 0.8139 (t60) REVERT: C 121 ASN cc_start: 0.9029 (m-40) cc_final: 0.8471 (m-40) REVERT: C 125 LYS cc_start: 0.9437 (mmmt) cc_final: 0.8932 (mmtp) REVERT: C 156 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8461 (mm-30) REVERT: C 165 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8297 (mmmm) REVERT: C 185 TYR cc_start: 0.8987 (m-80) cc_final: 0.8752 (m-80) REVERT: C 187 THR cc_start: 0.8885 (m) cc_final: 0.8648 (p) REVERT: D 16 HIS cc_start: 0.9084 (m170) cc_final: 0.8732 (m170) REVERT: D 27 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8751 (mmtm) REVERT: D 36 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8566 (mm) REVERT: D 72 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7786 (pm20) REVERT: D 110 ASP cc_start: 0.7821 (t0) cc_final: 0.7312 (t0) REVERT: D 138 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6652 (mp) REVERT: D 155 LEU cc_start: 0.9205 (mt) cc_final: 0.8971 (mt) REVERT: D 165 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8064 (mppt) REVERT: D 217 PHE cc_start: 0.8607 (m-80) cc_final: 0.8086 (m-80) REVERT: D 248 MET cc_start: 0.6392 (mmm) cc_final: 0.6086 (mmt) REVERT: D 295 MET cc_start: 0.8637 (mmm) cc_final: 0.8398 (mmm) REVERT: D 297 ASP cc_start: 0.8149 (p0) cc_final: 0.7910 (p0) REVERT: D 308 THR cc_start: 0.6986 (p) cc_final: 0.6700 (p) REVERT: D 311 ASN cc_start: 0.7739 (p0) cc_final: 0.6499 (t0) REVERT: D 340 GLN cc_start: 0.8627 (pt0) cc_final: 0.8416 (pm20) REVERT: D 352 MET cc_start: 0.8473 (pmm) cc_final: 0.8172 (ppp) REVERT: D 353 HIS cc_start: 0.6887 (m-70) cc_final: 0.6681 (m-70) REVERT: D 363 LEU cc_start: 0.9473 (mm) cc_final: 0.9227 (mm) REVERT: D 375 MET cc_start: 0.8442 (tmm) cc_final: 0.8150 (tmm) REVERT: D 376 MET cc_start: 0.8704 (ttt) cc_final: 0.8165 (tmm) REVERT: D 434 MET cc_start: 0.7436 (mmt) cc_final: 0.7071 (mtt) REVERT: D 441 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7347 (mp0) REVERT: E 2 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7942 (mp0) REVERT: E 87 GLU cc_start: 0.9115 (mp0) cc_final: 0.8684 (pm20) REVERT: E 148 ASP cc_start: 0.8589 (m-30) cc_final: 0.8381 (m-30) REVERT: E 201 GLU cc_start: 0.8460 (pp20) cc_final: 0.8215 (pp20) REVERT: E 261 ASP cc_start: 0.8750 (t0) cc_final: 0.7961 (p0) REVERT: E 285 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8489 (mm-30) REVERT: E 338 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: E 344 LEU cc_start: 0.9388 (tt) cc_final: 0.9028 (tp) REVERT: E 408 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8483 (tp) REVERT: E 482 LEU cc_start: 0.9085 (tp) cc_final: 0.8860 (tm) REVERT: E 485 GLN cc_start: 0.8706 (mt0) cc_final: 0.8149 (mp10) REVERT: E 486 PHE cc_start: 0.8877 (m-80) cc_final: 0.8447 (m-80) REVERT: E 487 ASP cc_start: 0.8785 (t0) cc_final: 0.8296 (p0) REVERT: E 489 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: E 614 TYR cc_start: 0.7936 (t80) cc_final: 0.7550 (t80) REVERT: E 624 ARG cc_start: 0.6800 (mtp85) cc_final: 0.6566 (ttt90) REVERT: E 684 MET cc_start: 0.8522 (mmm) cc_final: 0.7840 (tpp) REVERT: E 687 ARG cc_start: 0.7883 (mpp-170) cc_final: 0.7561 (mmp-170) REVERT: E 698 GLN cc_start: 0.7910 (tt0) cc_final: 0.7696 (pt0) REVERT: E 809 TYR cc_start: 0.8515 (m-80) cc_final: 0.8091 (m-80) REVERT: F 355 LEU cc_start: 0.9467 (mt) cc_final: 0.9130 (mt) REVERT: F 377 PHE cc_start: 0.9210 (m-80) cc_final: 0.8946 (m-80) REVERT: F 451 ASP cc_start: 0.9047 (m-30) cc_final: 0.8739 (t0) REVERT: F 513 THR cc_start: 0.9083 (p) cc_final: 0.8452 (t) REVERT: F 517 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8873 (pt0) REVERT: F 527 HIS cc_start: 0.8976 (m170) cc_final: 0.8739 (m170) REVERT: F 528 LEU cc_start: 0.9084 (tp) cc_final: 0.8737 (tp) REVERT: F 533 ARG cc_start: 0.8703 (ptt90) cc_final: 0.8440 (ptt90) REVERT: F 615 LYS cc_start: 0.8613 (mttt) cc_final: 0.8219 (mtmm) REVERT: F 643 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8878 (mm-40) REVERT: F 651 TYR cc_start: 0.9095 (t80) cc_final: 0.8861 (t80) REVERT: F 659 GLU cc_start: 0.8975 (tp30) cc_final: 0.8704 (mm-30) REVERT: F 663 GLU cc_start: 0.9184 (tp30) cc_final: 0.8773 (tp30) REVERT: F 666 ARG cc_start: 0.9183 (ttm-80) cc_final: 0.8756 (mtm110) REVERT: F 680 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8093 (p0) REVERT: F 689 ILE cc_start: 0.8970 (mt) cc_final: 0.8764 (mp) REVERT: F 717 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8222 (tmmm) REVERT: F 726 SER cc_start: 0.9323 (t) cc_final: 0.9064 (p) REVERT: F 821 ASP cc_start: 0.8515 (m-30) cc_final: 0.8050 (p0) REVERT: F 830 LEU cc_start: 0.9121 (mt) cc_final: 0.8714 (tp) REVERT: G 50 ASP cc_start: 0.9367 (m-30) cc_final: 0.8970 (p0) REVERT: G 144 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8466 (mmt-90) REVERT: G 152 LYS cc_start: 0.8679 (tmmm) cc_final: 0.8377 (tmmt) REVERT: G 342 ASN cc_start: 0.8919 (m-40) cc_final: 0.8232 (t0) REVERT: G 450 TYR cc_start: 0.7909 (m-10) cc_final: 0.7646 (m-10) REVERT: G 468 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8923 (pt0) REVERT: G 487 ASP cc_start: 0.8758 (t0) cc_final: 0.8445 (t0) REVERT: G 594 TYR cc_start: 0.9233 (t80) cc_final: 0.8834 (t80) REVERT: G 642 THR cc_start: 0.9419 (p) cc_final: 0.9207 (t) REVERT: G 645 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8725 (tt0) REVERT: G 687 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8449 (ptp-170) REVERT: G 692 LEU cc_start: 0.9349 (mt) cc_final: 0.9099 (mm) REVERT: G 709 PHE cc_start: 0.8869 (t80) cc_final: 0.8630 (t80) REVERT: G 719 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7707 (mm110) REVERT: G 784 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8752 (tp-100) REVERT: G 806 ARG cc_start: 0.8850 (ttp-170) cc_final: 0.8534 (ptp-170) REVERT: H 239 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: H 273 SER cc_start: 0.8775 (m) cc_final: 0.8516 (t) REVERT: H 289 GLU cc_start: 0.8763 (tp30) cc_final: 0.8429 (tp30) REVERT: H 306 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: H 315 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8198 (mm-30) REVERT: H 420 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8328 (tm-30) REVERT: H 423 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7911 (t0) REVERT: H 509 ASN cc_start: 0.8399 (m110) cc_final: 0.8158 (m-40) REVERT: H 527 HIS cc_start: 0.7527 (m-70) cc_final: 0.6939 (m-70) REVERT: H 529 MET cc_start: 0.8552 (tmm) cc_final: 0.8115 (tmm) REVERT: H 592 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7032 (mtt-85) REVERT: H 604 MET cc_start: 0.7690 (tmt) cc_final: 0.7108 (tmm) REVERT: H 642 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: H 662 LYS cc_start: 0.9302 (tppp) cc_final: 0.8835 (tptp) REVERT: H 690 GLU cc_start: 0.7811 (pp20) cc_final: 0.7430 (pp20) REVERT: H 717 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7851 (tmmt) REVERT: H 725 GLU cc_start: 0.8946 (tt0) cc_final: 0.8667 (tp30) REVERT: H 729 ASN cc_start: 0.9199 (m-40) cc_final: 0.8905 (m-40) REVERT: H 784 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: H 790 MET cc_start: 0.6983 (tmm) cc_final: 0.6302 (mpt) REVERT: H 836 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: H 844 SER cc_start: 0.9221 (t) cc_final: 0.8823 (p) REVERT: K 122 GLN cc_start: 0.8495 (tp40) cc_final: 0.8082 (tm-30) REVERT: K 130 LYS cc_start: 0.9352 (ttmt) cc_final: 0.8980 (tttp) REVERT: K 132 GLU cc_start: 0.9011 (tp30) cc_final: 0.8391 (tm-30) REVERT: K 149 THR cc_start: 0.6812 (p) cc_final: 0.6556 (p) REVERT: Y 117 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7474 (pp30) REVERT: Y 133 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8372 (mpp80) REVERT: Y 136 ARG cc_start: 0.8721 (ttm110) cc_final: 0.8091 (ptp-110) outliers start: 118 outliers final: 67 residues processed: 1024 average time/residue: 0.6378 time to fit residues: 816.7362 Evaluate side-chains 977 residues out of total 4444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 884 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 437 TYR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 619 HIS Chi-restraints excluded: chain E residue 663 TYR Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 379 TYR Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 643 GLN Chi-restraints excluded: chain F residue 647 LYS Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 696 THR Chi-restraints excluded: chain F residue 717 LYS Chi-restraints excluded: chain F residue 727 VAL Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain G residue 123 TYR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 632 LEU Chi-restraints excluded: chain G residue 687 ARG Chi-restraints excluded: chain G residue 711 LYS Chi-restraints excluded: chain G residue 719 GLN Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 784 GLN Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 277 VAL Chi-restraints excluded: chain H residue 306 GLU Chi-restraints excluded: chain H residue 344 GLU Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 423 ASN Chi-restraints excluded: chain H residue 500 LEU Chi-restraints excluded: chain H residue 523 SER Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 681 LEU Chi-restraints excluded: chain H residue 717 LYS Chi-restraints excluded: chain H residue 736 LEU Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 784 TYR Chi-restraints excluded: chain H residue 836 GLU Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 117 GLN Chi-restraints excluded: chain Y residue 126 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 196 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 464 optimal weight: 1.9990 chunk 272 optimal weight: 0.0870 chunk 245 optimal weight: 3.9990 chunk 416 optimal weight: 0.5980 chunk 302 optimal weight: 0.7980 chunk 199 optimal weight: 0.3980 chunk 183 optimal weight: 0.6980 chunk 348 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 226 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 GLN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN ** G 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.139168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097476 restraints weight = 80732.204| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.69 r_work: 0.3230 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.257 40159 Z= 0.250 Angle : 0.970 59.182 54339 Z= 0.485 Chirality : 0.051 1.593 6052 Planarity : 0.005 0.111 6995 Dihedral : 7.655 179.030 5316 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.75 % Rotamer: Outliers : 2.64 % Allowed : 28.50 % Favored : 68.86 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.12), residues: 4773 helix: 1.54 (0.10), residues: 2747 sheet: -0.79 (0.28), residues: 329 loop : -0.71 (0.16), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG H 827 TYR 0.038 0.001 TYR F 816 PHE 0.108 0.002 PHE E 465 TRP 0.033 0.002 TRP D 105 HIS 0.009 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00563 (40155) covalent geometry : angle 0.97036 (54339) hydrogen bonds : bond 0.04370 ( 2274) hydrogen bonds : angle 4.61448 ( 6699) Misc. bond : bond 0.00046 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21438.80 seconds wall clock time: 364 minutes 20.30 seconds (21860.30 seconds total)