Starting phenix.real_space_refine on Wed May 28 23:19:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wp2_37708/05_2025/8wp2_37708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wp2_37708/05_2025/8wp2_37708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wp2_37708/05_2025/8wp2_37708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wp2_37708/05_2025/8wp2_37708.map" model { file = "/net/cci-nas-00/data/ceres_data/8wp2_37708/05_2025/8wp2_37708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wp2_37708/05_2025/8wp2_37708.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.032 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 150 5.49 5 S 91 5.16 5 C 19903 2.51 5 N 5273 2.21 5 O 6127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31544 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3682 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3421 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 405} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3618 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 2 Chain: "D" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3454 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 405} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 341 Classifications: {'DNA': 11, 'RNA': 6} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 11, 'RNA': 7} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "I" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3700 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain breaks: 2 Chain: "J" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 406} Chain: "K" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3709 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 436} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3420 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 405} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 11, 'RNA': 7} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "N" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "O" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 341 Classifications: {'DNA': 11, 'RNA': 6} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Residues with excluded nonbonded symmetry interactions: 209 residue: pdb=" N GLU A 9 " occ=0.06 ... (7 atoms not shown) pdb=" OE2 GLU A 9 " occ=0.00 residue: pdb=" N LYS A 235 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 235 " occ=0.69 residue: pdb=" N ALA A 237 " occ=0.41 ... (3 atoms not shown) pdb=" CB ALA A 237 " occ=0.57 residue: pdb=" N ARG A 243 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 243 " occ=0.08 residue: pdb=" N ASP A 244 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 244 " occ=0.55 residue: pdb=" N LYS A 290 " occ=0.88 ... (7 atoms not shown) pdb=" NZ LYS A 290 " occ=0.45 residue: pdb=" N ASN A 293 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 293 " occ=0.39 residue: pdb=" N GLY A 318 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 318 " occ=0.56 residue: pdb=" N THR A 431 " occ=0.75 ... (5 atoms not shown) pdb=" CG2 THR A 431 " occ=0.76 residue: pdb=" N SER B 163 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER B 163 " occ=0.00 residue: pdb=" N VAL B 208 " occ=0.10 ... (5 atoms not shown) pdb=" CG2 VAL B 208 " occ=0.38 residue: pdb=" N GLY B 249 " occ=0.38 ... (2 atoms not shown) pdb=" O GLY B 249 " occ=0.91 ... (remaining 197 not shown) Time building chain proxies: 18.96, per 1000 atoms: 0.60 Number of scatterers: 31544 At special positions: 0 Unit cell: (116.55, 168, 218.4, 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 91 16.00 P 150 15.00 O 6127 8.00 N 5273 7.00 C 19903 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=0, symmetry=0 Time building additional restraints: 7.34 Conformation dependent library (CDL) restraints added in 3.4 seconds 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6660 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 49 sheets defined 35.8% alpha, 13.6% beta 18 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 10.60 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.966A pdb=" N LEU A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 removed outlier: 4.096A pdb=" N LEU A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.579A pdb=" N PHE A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 131 removed outlier: 3.676A pdb=" N PHE A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.608A pdb=" N TYR A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.618A pdb=" N ARG A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.581A pdb=" N ALA A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.131A pdb=" N LYS A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 removed outlier: 4.680A pdb=" N ALA A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.952A pdb=" N LYS A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.530A pdb=" N GLY A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.806A pdb=" N ASP B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN B 15 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP B 16 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP B 20 " --> pdb=" O ASP B 16 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 55 removed outlier: 3.537A pdb=" N ASN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.550A pdb=" N GLU B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.664A pdb=" N ILE B 94 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.499A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.767A pdb=" N LEU B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.805A pdb=" N PHE B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.544A pdb=" N LYS B 237 " --> pdb=" O HIS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.741A pdb=" N ARG B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 265 " --> pdb=" O CYS B 261 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.513A pdb=" N MET B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.962A pdb=" N ARG B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.576A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.649A pdb=" N GLY C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 61 removed outlier: 4.395A pdb=" N LYS C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 56 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 97 through 104 removed outlier: 4.231A pdb=" N PHE C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 131 removed outlier: 3.704A pdb=" N THR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 122 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.632A pdb=" N LYS C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.646A pdb=" N LEU C 214 " --> pdb=" O PHE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 331 through 344 removed outlier: 4.231A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 removed outlier: 4.249A pdb=" N GLU C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 377 removed outlier: 3.858A pdb=" N ASP C 371 " --> pdb=" O HIS C 367 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA C 372 " --> pdb=" O GLN C 368 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.559A pdb=" N SER C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 removed outlier: 3.948A pdb=" N ASP C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 486 " --> pdb=" O PHE C 482 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 489 " --> pdb=" O LYS C 485 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER C 493 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'D' and resid 17 through 26 removed outlier: 3.616A pdb=" N LEU D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 71 through 88 removed outlier: 3.527A pdb=" N LYS D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 139 Processing helix chain 'D' and resid 147 through 157 removed outlier: 3.527A pdb=" N ASN D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.554A pdb=" N PHE D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 233 removed outlier: 4.427A pdb=" N THR D 232 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 243 through 247 Processing helix chain 'D' and resid 257 through 278 removed outlier: 3.761A pdb=" N VAL D 266 " --> pdb=" O LYS D 262 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 267 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.505A pdb=" N GLN D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER D 360 " --> pdb=" O VAL D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.848A pdb=" N LYS D 366 " --> pdb=" O ARG D 363 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP D 368 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 385 removed outlier: 3.950A pdb=" N LYS D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 377 " --> pdb=" O TRP D 373 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE D 380 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 22 through 30 Processing helix chain 'I' and resid 46 through 61 removed outlier: 3.864A pdb=" N LYS I 51 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE I 52 " --> pdb=" O GLN I 48 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR I 56 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 83 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.969A pdb=" N TYR I 106 " --> pdb=" O GLY I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 132 removed outlier: 4.002A pdb=" N THR I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER I 127 " --> pdb=" O ASP I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 151 removed outlier: 4.219A pdb=" N TYR I 148 " --> pdb=" O PRO I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 218 removed outlier: 3.560A pdb=" N GLN I 209 " --> pdb=" O GLN I 205 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU I 214 " --> pdb=" O PHE I 210 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS I 216 " --> pdb=" O ALA I 212 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS I 217 " --> pdb=" O ARG I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 263 removed outlier: 3.936A pdb=" N GLY I 250 " --> pdb=" O SER I 246 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N HIS I 251 " --> pdb=" O LYS I 247 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP I 254 " --> pdb=" O GLY I 250 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS I 263 " --> pdb=" O ALA I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 343 removed outlier: 3.881A pdb=" N ALA I 337 " --> pdb=" O LYS I 333 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 350 removed outlier: 4.155A pdb=" N GLU I 348 " --> pdb=" O GLN I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 376 removed outlier: 3.695A pdb=" N GLU I 375 " --> pdb=" O ASP I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 462 Processing helix chain 'I' and resid 477 through 490 removed outlier: 3.841A pdb=" N ALA I 483 " --> pdb=" O THR I 479 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP I 484 " --> pdb=" O LEU I 480 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS I 485 " --> pdb=" O ARG I 481 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE I 486 " --> pdb=" O PHE I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 506 removed outlier: 4.060A pdb=" N TYR I 505 " --> pdb=" O ALA I 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 71 through 88 removed outlier: 3.908A pdb=" N LYS J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN J 87 " --> pdb=" O LYS J 83 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 138 removed outlier: 3.675A pdb=" N GLY J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 157 Processing helix chain 'J' and resid 199 through 203 Processing helix chain 'J' and resid 234 through 238 Processing helix chain 'J' and resid 243 through 249 Processing helix chain 'J' and resid 257 through 280 removed outlier: 3.571A pdb=" N ILE J 265 " --> pdb=" O CYS J 261 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS J 278 " --> pdb=" O GLU J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 353 through 365 Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'J' and resid 369 through 384 removed outlier: 3.561A pdb=" N LYS J 376 " --> pdb=" O THR J 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 47 through 57 removed outlier: 4.099A pdb=" N LYS K 51 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE K 52 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 97 through 106 removed outlier: 3.542A pdb=" N PHE K 104 " --> pdb=" O ASP K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 131 removed outlier: 4.899A pdb=" N TYR K 115 " --> pdb=" O HIS K 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL K 118 " --> pdb=" O THR K 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE K 121 " --> pdb=" O LEU K 117 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 151 removed outlier: 3.691A pdb=" N TYR K 148 " --> pdb=" O PRO K 144 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR K 150 " --> pdb=" O GLU K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 213 removed outlier: 3.511A pdb=" N LYS K 211 " --> pdb=" O HIS K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 230 Processing helix chain 'K' and resid 250 through 263 removed outlier: 3.512A pdb=" N LYS K 263 " --> pdb=" O ALA K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 351 removed outlier: 3.601A pdb=" N LYS K 336 " --> pdb=" O PRO K 332 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA K 337 " --> pdb=" O LYS K 333 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER K 340 " --> pdb=" O LYS K 336 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR K 346 " --> pdb=" O SER K 342 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN K 349 " --> pdb=" O SER K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 377 removed outlier: 4.746A pdb=" N ALA K 372 " --> pdb=" O GLN K 368 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE K 373 " --> pdb=" O GLU K 369 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU K 375 " --> pdb=" O ASP K 371 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL K 376 " --> pdb=" O ALA K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 460 removed outlier: 3.596A pdb=" N LYS K 457 " --> pdb=" O LYS K 453 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP K 458 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE K 459 " --> pdb=" O VAL K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 477 through 491 removed outlier: 4.264A pdb=" N ALA K 483 " --> pdb=" O THR K 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 486 " --> pdb=" O PHE K 482 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY K 487 " --> pdb=" O ALA K 483 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 506 Processing helix chain 'L' and resid 13 through 29 removed outlier: 3.758A pdb=" N PHE L 17 " --> pdb=" O ASP L 13 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 55 removed outlier: 3.916A pdb=" N ILE L 49 " --> pdb=" O PHE L 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU L 50 " --> pdb=" O TRP L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 89 removed outlier: 4.357A pdb=" N LYS L 86 " --> pdb=" O ALA L 82 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN L 87 " --> pdb=" O LYS L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.859A pdb=" N ILE L 94 " --> pdb=" O ASP L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 114 removed outlier: 3.922A pdb=" N ARG L 114 " --> pdb=" O ILE L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 139 Processing helix chain 'L' and resid 147 through 157 Processing helix chain 'L' and resid 219 through 224 removed outlier: 4.137A pdb=" N THR L 224 " --> pdb=" O TYR L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 233 Processing helix chain 'L' and resid 234 through 238 Processing helix chain 'L' and resid 243 through 248 Processing helix chain 'L' and resid 257 through 280 removed outlier: 3.641A pdb=" N VAL L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN L 267 " --> pdb=" O ARG L 263 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU L 269 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU L 274 " --> pdb=" O ASN L 270 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG L 276 " --> pdb=" O ALA L 272 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET L 277 " --> pdb=" O PHE L 273 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP L 279 " --> pdb=" O LEU L 275 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS L 280 " --> pdb=" O ARG L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 302 No H-bonds generated for 'chain 'L' and resid 300 through 302' Processing helix chain 'L' and resid 353 through 360 removed outlier: 3.684A pdb=" N SER L 360 " --> pdb=" O VAL L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 382 removed outlier: 4.340A pdb=" N THR L 375 " --> pdb=" O ASN L 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.521A pdb=" N GLU A 444 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY A 385 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.817A pdb=" N ILE A 12 " --> pdb=" O CYS A 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 20 " --> pdb=" O ILE A 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 9.134A pdb=" N LYS A 94 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 43 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL A 141 " --> pdb=" O PHE A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 287 removed outlier: 3.776A pdb=" N GLU A 316 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA A 301 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS A 314 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET A 303 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL A 312 " --> pdb=" O MET A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.840A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LYS B 4 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE B 60 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE B 6 " --> pdb=" O PHE B 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 172 Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 328 removed outlier: 4.422A pdb=" N SER B 177 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE B 402 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AB1, first strand: chain 'B' and resid 283 through 286 Processing sheet with id=AB2, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AB3, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.401A pdb=" N LYS C 2 " --> pdb=" O LYS D 411 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE D 402 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER D 177 " --> pdb=" O SER D 404 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLU D 406 " --> pdb=" O TRP D 175 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TRP D 175 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL D 408 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 173 " --> pdb=" O VAL D 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.401A pdb=" N LYS C 2 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.569A pdb=" N GLN C 18 " --> pdb=" O PHE C 14 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.565A pdb=" N PHE C 224 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.650A pdb=" N ALA C 300 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AC2, first strand: chain 'C' and resid 356 through 359 removed outlier: 6.493A pdb=" N VAL C 357 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL C 386 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE C 359 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 5 through 6 removed outlier: 6.906A pdb=" N ILE D 5 " --> pdb=" O TRP D 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.505A pdb=" N ARG D 186 " --> pdb=" O THR D 216 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 239 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 292 through 294 removed outlier: 3.596A pdb=" N GLY D 312 " --> pdb=" O TRP D 319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 292 through 294 removed outlier: 3.696A pdb=" N ASN D 318 " --> pdb=" O THR D 344 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AC9, first strand: chain 'I' and resid 94 through 95 removed outlier: 3.785A pdb=" N LYS I 94 " --> pdb=" O VAL I 43 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY I 45 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP I 139 " --> pdb=" O GLN I 222 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N PHE I 224 " --> pdb=" O TRP I 139 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL I 141 " --> pdb=" O PHE I 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 302 through 304 removed outlier: 6.240A pdb=" N CYS I 279 " --> pdb=" O PHE I 358 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS I 360 " --> pdb=" O CYS I 279 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU I 281 " --> pdb=" O HIS I 360 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL I 357 " --> pdb=" O VAL I 384 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL I 386 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE I 359 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE I 388 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA I 361 " --> pdb=" O ILE I 388 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY I 385 " --> pdb=" O ASN I 446 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU I 444 " --> pdb=" O THR I 387 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER I 389 " --> pdb=" O PHE I 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AD3, first strand: chain 'I' and resid 397 through 398 removed outlier: 5.805A pdb=" N LYS J 167 " --> pdb=" O VAL J 414 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 31 through 33 removed outlier: 7.206A pdb=" N LYS J 4 " --> pdb=" O CYS J 58 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE J 60 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE J 6 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU J 62 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE J 118 " --> pdb=" O ILE J 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 175 through 177 removed outlier: 4.391A pdb=" N GLY J 325 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR J 291 " --> pdb=" O GLY J 325 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 175 through 177 Processing sheet with id=AD7, first strand: chain 'J' and resid 207 through 210 removed outlier: 3.665A pdb=" N TYR J 210 " --> pdb=" O TYR J 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 390 through 394 Processing sheet with id=AD9, first strand: chain 'K' and resid 396 through 398 removed outlier: 3.617A pdb=" N ILE K 5 " --> pdb=" O ALA K 410 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AE2, first strand: chain 'K' and resid 41 through 45 removed outlier: 6.915A pdb=" N GLY K 42 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE K 142 " --> pdb=" O GLY K 42 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE K 44 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP K 139 " --> pdb=" O GLN K 222 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE K 224 " --> pdb=" O TRP K 139 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL K 141 " --> pdb=" O PHE K 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 280 through 282 removed outlier: 3.523A pdb=" N TYR K 280 " --> pdb=" O PHE K 304 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 285 through 287 Processing sheet with id=AE5, first strand: chain 'K' and resid 356 through 361 removed outlier: 3.549A pdb=" N VAL K 357 " --> pdb=" O ASN K 382 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 419 through 420 removed outlier: 3.537A pdb=" N LEU K 420 " --> pdb=" O LEU K 441 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 32 through 33 removed outlier: 5.838A pdb=" N ILE L 5 " --> pdb=" O TRP L 33 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LYS L 4 " --> pdb=" O CYS L 58 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE L 60 " --> pdb=" O LYS L 4 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE L 6 " --> pdb=" O PHE L 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AE9, first strand: chain 'L' and resid 175 through 177 Processing sheet with id=AF1, first strand: chain 'L' and resid 207 through 210 removed outlier: 3.723A pdb=" N THR L 216 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG L 186 " --> pdb=" O THR L 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE L 187 " --> pdb=" O ILE L 239 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE L 239 " --> pdb=" O PHE L 187 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 284 through 286 removed outlier: 3.744A pdb=" N TYR L 293 " --> pdb=" O ILE L 323 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 304 through 305 removed outlier: 3.565A pdb=" N PHE L 305 " --> pdb=" O THR L 308 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 390 through 391 853 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 11.64 Time building geometry restraints manager: 8.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.96: 2 0.96 - 1.26: 4826 1.26 - 1.56: 27348 1.56 - 1.86: 436 1.86 - 2.16: 2 Bond restraints: 32614 Sorted by residual: bond pdb=" CG PRO C 144 " pdb=" CD PRO C 144 " ideal model delta sigma weight residual 1.503 0.653 0.850 3.40e-02 8.65e+02 6.24e+02 bond pdb=" CG PRO K 438 " pdb=" CD PRO K 438 " ideal model delta sigma weight residual 1.503 0.672 0.831 3.40e-02 8.65e+02 5.98e+02 bond pdb=" CB PRO K 438 " pdb=" CG PRO K 438 " ideal model delta sigma weight residual 1.492 2.162 -0.670 5.00e-02 4.00e+02 1.79e+02 bond pdb=" CB PRO C 144 " pdb=" CG PRO C 144 " ideal model delta sigma weight residual 1.492 2.035 -0.543 5.00e-02 4.00e+02 1.18e+02 bond pdb=" N PRO K 438 " pdb=" CD PRO K 438 " ideal model delta sigma weight residual 1.473 1.611 -0.138 1.40e-02 5.10e+03 9.71e+01 ... (remaining 32609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.92: 44675 8.92 - 17.84: 16 17.84 - 26.76: 6 26.76 - 35.68: 0 35.68 - 44.61: 1 Bond angle restraints: 44698 Sorted by residual: angle pdb=" N PRO C 144 " pdb=" CD PRO C 144 " pdb=" CG PRO C 144 " ideal model delta sigma weight residual 103.20 76.92 26.28 1.50e+00 4.44e-01 3.07e+02 angle pdb=" N PRO K 438 " pdb=" CD PRO K 438 " pdb=" CG PRO K 438 " ideal model delta sigma weight residual 103.20 79.99 23.21 1.50e+00 4.44e-01 2.39e+02 angle pdb=" CB PRO K 438 " pdb=" CG PRO K 438 " pdb=" CD PRO K 438 " ideal model delta sigma weight residual 106.10 61.49 44.61 3.20e+00 9.77e-02 1.94e+02 angle pdb=" CA PRO C 427 " pdb=" N PRO C 427 " pdb=" CD PRO C 427 " ideal model delta sigma weight residual 112.00 93.24 18.76 1.40e+00 5.10e-01 1.79e+02 angle pdb=" CA PRO K 438 " pdb=" N PRO K 438 " pdb=" CD PRO K 438 " ideal model delta sigma weight residual 112.00 94.26 17.74 1.40e+00 5.10e-01 1.60e+02 ... (remaining 44693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 18229 35.91 - 71.82: 991 71.82 - 107.73: 37 107.73 - 143.64: 9 143.64 - 179.55: 7 Dihedral angle restraints: 19273 sinusoidal: 8974 harmonic: 10299 Sorted by residual: dihedral pdb=" N PRO K 438 " pdb=" C PRO K 438 " pdb=" CA PRO K 438 " pdb=" CB PRO K 438 " ideal model delta harmonic sigma weight residual 115.10 103.40 11.70 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" CA PHE I 503 " pdb=" C PHE I 503 " pdb=" N LYS I 504 " pdb=" CA LYS I 504 " ideal model delta harmonic sigma weight residual 180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LYS L 313 " pdb=" C LYS L 313 " pdb=" N GLN L 314 " pdb=" CA GLN L 314 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 19270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4141 0.058 - 0.115: 625 0.115 - 0.173: 77 0.173 - 0.230: 11 0.230 - 0.288: 4 Chirality restraints: 4858 Sorted by residual: chirality pdb=" CB VAL C 412 " pdb=" CA VAL C 412 " pdb=" CG1 VAL C 412 " pdb=" CG2 VAL C 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PRO A 323 " pdb=" N PRO A 323 " pdb=" C PRO A 323 " pdb=" CB PRO A 323 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1' U M 18 " pdb=" O4' U M 18 " pdb=" C2' U M 18 " pdb=" N1 U M 18 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 4855 not shown) Planarity restraints: 5130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 426 " -0.115 5.00e-02 4.00e+02 1.55e-01 3.84e+01 pdb=" N PRO C 427 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO C 427 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 427 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 143 " -0.101 5.00e-02 4.00e+02 1.37e-01 2.98e+01 pdb=" N PRO C 144 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO C 144 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO C 144 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 152 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO I 153 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO I 153 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO I 153 " 0.055 5.00e-02 4.00e+02 ... (remaining 5127 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 937 2.67 - 3.23: 31061 3.23 - 3.79: 53578 3.79 - 4.34: 72958 4.34 - 4.90: 111978 Nonbonded interactions: 270512 Sorted by model distance: nonbonded pdb=" OG1 THR C 399 " pdb=" OE1 GLU C 400 " model vdw 2.114 3.040 nonbonded pdb=" O TYR C 403 " pdb=" OH TYR D 416 " model vdw 2.143 3.040 nonbonded pdb=" OG SER D 288 " pdb=" OP2 U G 10 " model vdw 2.160 3.040 nonbonded pdb=" OG SER L 288 " pdb=" OP2 U O 10 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR I 505 " pdb=" O ASN K 129 " model vdw 2.170 3.040 ... (remaining 270507 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 4 through 153 or resid 203 through 319 or resid 328 throug \ h 506)) selection = (chain 'C' and (resid 4 through 286 or (resid 287 and (name N or name CA or name \ C or name O or name CB )) or resid 288 through 318 or (resid 319 and (name N or \ name CA or name C or name O or name CB )) or resid 328 through 506)) selection = (chain 'I' and (resid 4 through 153 or resid 203 through 286 or (resid 287 and ( \ name N or name CA or name C or name O or name CB )) or resid 288 through 318 or \ (resid 319 and (name N or name CA or name C or name O or name CB )) or resid 328 \ through 506)) selection = (chain 'K' and (resid 4 through 153 or resid 203 through 318 or (resid 319 and ( \ name N or name CA or name C or name O or name CB )) or resid 328 through 506)) } ncs_group { reference = (chain 'B' and (resid 2 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 417)) selection = (chain 'D' and (resid 2 through 145 or (resid 146 through 163 and (name N or nam \ e CA or name C or name O or name CB )) or resid 164 through 417)) selection = (chain 'J' and (resid 2 through 145 or (resid 146 through 163 and (name N or nam \ e CA or name C or name O or name CB )) or resid 164 through 417)) selection = (chain 'L' and resid 2 through 417) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 1 through 17) selection = (chain 'M' and resid 1 through 17) selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.84 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.140 Check model and map are aligned: 0.170 Set scattering table: 0.280 Process input model: 74.330 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.140 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 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 : 0.009 0.850 32614 Z= 0.282 Angle : 0.783 44.606 44698 Z= 0.423 Chirality : 0.043 0.288 4858 Planarity : 0.006 0.155 5130 Dihedral : 20.041 179.551 12613 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.56 % Favored : 92.18 % Rotamer: Outliers : 0.23 % Allowed : 30.38 % Favored : 69.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.14), residues: 3466 helix: -1.64 (0.15), residues: 981 sheet: -2.20 (0.23), residues: 469 loop : -1.51 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 124 HIS 0.006 0.001 HIS C 360 PHE 0.030 0.002 PHE I 304 TYR 0.022 0.001 TYR C 397 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.30142 ( 875) hydrogen bonds : angle 10.41487 ( 2415) covalent geometry : bond 0.00897 (32614) covalent geometry : angle 0.78341 (44698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 265 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7648 (mm) cc_final: 0.7405 (mm) REVERT: A 457 LYS cc_start: 0.5402 (OUTLIER) cc_final: 0.5081 (mmpt) REVERT: B 71 ARG cc_start: 0.6224 (mmt90) cc_final: 0.5870 (mmt90) REVERT: B 277 MET cc_start: 0.2054 (mpp) cc_final: 0.1450 (mpp) REVERT: B 352 ASP cc_start: 0.7718 (t0) cc_final: 0.7349 (p0) REVERT: C 59 HIS cc_start: 0.7208 (t-90) cc_final: 0.6893 (t-170) REVERT: C 460 LEU cc_start: 0.5042 (tp) cc_final: 0.4809 (tp) REVERT: D 319 TRP cc_start: 0.5573 (p-90) cc_final: 0.4755 (p-90) REVERT: D 382 LYS cc_start: 0.7331 (mmpt) cc_final: 0.7082 (mmpt) REVERT: D 392 TYR cc_start: 0.7788 (p90) cc_final: 0.7301 (p90) REVERT: I 121 PHE cc_start: 0.7686 (m-80) cc_final: 0.7405 (m-80) REVERT: I 251 HIS cc_start: 0.5643 (p90) cc_final: 0.4962 (p-80) REVERT: L 102 GLN cc_start: 0.7305 (mm-40) cc_final: 0.6608 (tp40) REVERT: L 256 ILE cc_start: 0.4025 (tp) cc_final: 0.3788 (mm) outliers start: 7 outliers final: 2 residues processed: 270 average time/residue: 0.4278 time to fit residues: 186.0297 Evaluate side-chains 248 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain J residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 279 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 323 optimal weight: 40.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 ASN A 209 GLN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 98 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS I 209 GLN I 341 GLN I 466 ASN ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 HIS ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 ASN K 111 HIS K 207 HIS ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN L 174 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.117450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.101047 restraints weight = 96235.611| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.62 r_work: 0.4096 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2762 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2841 | |-----------------------------------------------------------------------------| r_final: 0.4086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 32614 Z= 0.271 Angle : 0.782 11.393 44698 Z= 0.404 Chirality : 0.050 0.441 4858 Planarity : 0.006 0.070 5130 Dihedral : 18.011 177.778 5587 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.17 % Favored : 90.57 % Rotamer: Outliers : 5.09 % Allowed : 26.95 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.14), residues: 3466 helix: -1.70 (0.14), residues: 1088 sheet: -2.15 (0.24), residues: 446 loop : -1.71 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP L 319 HIS 0.014 0.002 HIS K 16 PHE 0.032 0.003 PHE J 17 TYR 0.028 0.002 TYR K 467 ARG 0.012 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.06699 ( 875) hydrogen bonds : angle 6.81928 ( 2415) covalent geometry : bond 0.00616 (32614) covalent geometry : angle 0.78236 (44698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 285 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 MET cc_start: 0.7673 (ppp) cc_final: 0.7245 (ppp) REVERT: B 410 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5874 (m-80) REVERT: C 59 HIS cc_start: 0.7515 (t-90) cc_final: 0.7121 (t-170) REVERT: C 309 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.6236 (m-30) REVERT: C 505 TYR cc_start: 0.3282 (OUTLIER) cc_final: 0.1241 (m-80) REVERT: D 260 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6552 (mm-30) REVERT: D 277 MET cc_start: 0.7471 (tpt) cc_final: 0.7024 (tpt) REVERT: I 91 ILE cc_start: 0.5827 (OUTLIER) cc_final: 0.5462 (mm) REVERT: I 92 THR cc_start: 0.6751 (OUTLIER) cc_final: 0.6535 (p) REVERT: I 224 PHE cc_start: 0.6716 (m-80) cc_final: 0.6407 (m-80) REVERT: I 430 GLN cc_start: 0.6040 (OUTLIER) cc_final: 0.5820 (mt0) REVERT: I 462 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7294 (mt) REVERT: J 154 TYR cc_start: 0.5045 (t80) cc_final: 0.4697 (t80) REVERT: K 141 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8197 (m) REVERT: L 102 GLN cc_start: 0.7527 (mm-40) cc_final: 0.6720 (tp40) REVERT: L 176 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7058 (mp) REVERT: L 231 GLU cc_start: 0.6414 (pm20) cc_final: 0.5118 (pm20) outliers start: 157 outliers final: 75 residues processed: 414 average time/residue: 0.4286 time to fit residues: 286.3864 Evaluate side-chains 341 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 256 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 413 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 462 LEU Chi-restraints excluded: chain I residue 470 CYS Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 234 HIS Chi-restraints excluded: chain L residue 309 MET Chi-restraints excluded: chain L residue 334 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 307 optimal weight: 0.9990 chunk 169 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 249 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 98 ASN C 207 HIS C 209 GLN C 344 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 ASN I 209 GLN I 296 ASN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS K 251 HIS L 48 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.118978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.102077 restraints weight = 97853.079| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.74 r_work: 0.4129 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4126 r_free = 0.4126 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2841 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2900 | |-----------------------------------------------------------------------------| r_final: 0.4116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32614 Z= 0.158 Angle : 0.660 10.842 44698 Z= 0.339 Chirality : 0.046 0.314 4858 Planarity : 0.005 0.061 5130 Dihedral : 17.835 179.720 5581 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.91 % Favored : 91.83 % Rotamer: Outliers : 4.25 % Allowed : 28.47 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.14), residues: 3466 helix: -1.53 (0.14), residues: 1081 sheet: -1.98 (0.23), residues: 485 loop : -1.65 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 319 HIS 0.005 0.001 HIS K 16 PHE 0.022 0.002 PHE J 17 TYR 0.021 0.001 TYR C 467 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05293 ( 875) hydrogen bonds : angle 6.12354 ( 2415) covalent geometry : bond 0.00356 (32614) covalent geometry : angle 0.65992 (44698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 278 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6652 (mt) REVERT: A 210 PHE cc_start: 0.6010 (m-80) cc_final: 0.5573 (m-80) REVERT: B 122 MET cc_start: 0.7736 (ppp) cc_final: 0.7290 (ppp) REVERT: B 169 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6069 (mm-30) REVERT: B 352 ASP cc_start: 0.8118 (t0) cc_final: 0.7654 (p0) REVERT: B 410 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.5482 (m-10) REVERT: B 416 TYR cc_start: 0.6282 (t80) cc_final: 0.6024 (t80) REVERT: C 59 HIS cc_start: 0.7563 (t-90) cc_final: 0.7150 (t-170) REVERT: C 365 PHE cc_start: 0.4974 (m-80) cc_final: 0.4640 (m-10) REVERT: D 33 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.7816 (m100) REVERT: D 251 TYR cc_start: 0.6310 (t80) cc_final: 0.5987 (t80) REVERT: D 260 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6549 (mm-30) REVERT: D 277 MET cc_start: 0.7447 (tpt) cc_final: 0.6913 (tpt) REVERT: D 309 MET cc_start: 0.6133 (tpt) cc_final: 0.4949 (tpt) REVERT: D 369 TRP cc_start: 0.3984 (m-90) cc_final: 0.3516 (m-90) REVERT: I 91 ILE cc_start: 0.5527 (OUTLIER) cc_final: 0.5299 (mt) REVERT: I 142 ILE cc_start: 0.7537 (mp) cc_final: 0.7300 (mt) REVERT: I 223 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7566 (tt) REVERT: I 224 PHE cc_start: 0.6505 (m-80) cc_final: 0.6299 (m-10) REVERT: I 248 ILE cc_start: 0.7071 (tt) cc_final: 0.6818 (mp) REVERT: J 154 TYR cc_start: 0.4806 (t80) cc_final: 0.4415 (t80) REVERT: J 278 LYS cc_start: 0.7814 (tppt) cc_final: 0.7410 (mmtt) REVERT: K 141 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8093 (m) REVERT: K 479 THR cc_start: 0.5406 (OUTLIER) cc_final: 0.4578 (p) REVERT: L 102 GLN cc_start: 0.7610 (mm-40) cc_final: 0.6733 (tp40) REVERT: L 231 GLU cc_start: 0.6490 (pm20) cc_final: 0.5576 (pm20) outliers start: 131 outliers final: 65 residues processed: 392 average time/residue: 0.4134 time to fit residues: 260.0899 Evaluate side-chains 338 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 229 LEU Chi-restraints excluded: chain K residue 251 HIS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 362 LYS Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 479 THR Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 234 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 348 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 332 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 355 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN A 322 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 98 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 439 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 ASN I 131 ASN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN K 207 HIS ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN ** L 370 ASN ** 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 = 0.4540 r_free = 0.4540 target = 0.115258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.097905 restraints weight = 96127.672| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.36 r_work: 0.4046 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2900 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2941 | |-----------------------------------------------------------------------------| r_final: 0.4039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.144 32614 Z= 0.312 Angle : 0.822 12.794 44698 Z= 0.422 Chirality : 0.052 0.519 4858 Planarity : 0.006 0.069 5130 Dihedral : 18.308 176.891 5581 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.95 % Favored : 89.73 % Rotamer: Outliers : 6.94 % Allowed : 27.17 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.13), residues: 3466 helix: -1.76 (0.14), residues: 1113 sheet: -2.19 (0.23), residues: 435 loop : -1.96 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP I 269 HIS 0.019 0.002 HIS K 251 PHE 0.035 0.003 PHE I 419 TYR 0.033 0.002 TYR I 467 ARG 0.010 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.05984 ( 875) hydrogen bonds : angle 6.40608 ( 2415) covalent geometry : bond 0.00710 (32614) covalent geometry : angle 0.82207 (44698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 305 time to evaluate : 3.200 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: A 16 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.5300 (p90) REVERT: A 101 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6975 (mt) REVERT: A 122 ILE cc_start: 0.7074 (mm) cc_final: 0.6640 (mt) REVERT: B 122 MET cc_start: 0.7733 (ppp) cc_final: 0.7445 (ppp) REVERT: B 169 GLU cc_start: 0.6269 (mm-30) cc_final: 0.5850 (mm-30) REVERT: B 277 MET cc_start: 0.3193 (mpp) cc_final: 0.2205 (mpp) REVERT: B 410 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: C 13 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7368 (mp) REVERT: C 59 HIS cc_start: 0.7597 (t-90) cc_final: 0.7196 (t-170) REVERT: C 74 MET cc_start: 0.3443 (OUTLIER) cc_final: 0.3201 (ttt) REVERT: C 121 PHE cc_start: 0.5722 (m-80) cc_final: 0.5481 (m-80) REVERT: C 407 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6635 (ptt180) REVERT: C 505 TYR cc_start: 0.3187 (OUTLIER) cc_final: 0.1119 (m-80) REVERT: D 260 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6558 (mm-30) REVERT: I 85 LYS cc_start: 0.5940 (OUTLIER) cc_final: 0.5395 (mtmm) REVERT: I 91 ILE cc_start: 0.5549 (OUTLIER) cc_final: 0.5128 (mm) REVERT: I 113 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5741 (ptm160) REVERT: I 142 ILE cc_start: 0.7518 (mp) cc_final: 0.7268 (mt) REVERT: I 146 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7490 (mm-30) REVERT: I 161 MET cc_start: 0.4910 (ptm) cc_final: 0.4436 (ptp) REVERT: I 224 PHE cc_start: 0.7034 (m-80) cc_final: 0.6124 (m-80) REVERT: I 231 TRP cc_start: 0.7406 (p-90) cc_final: 0.6837 (p-90) REVERT: I 430 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5850 (mt0) REVERT: I 471 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.6010 (pt) REVERT: J 154 TYR cc_start: 0.4913 (t80) cc_final: 0.4506 (t80) REVERT: J 391 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.5235 (t80) REVERT: K 141 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8183 (m) REVERT: K 150 TYR cc_start: 0.4613 (OUTLIER) cc_final: 0.4214 (m-10) REVERT: L 20 TRP cc_start: 0.1782 (OUTLIER) cc_final: -0.0530 (t60) REVERT: L 34 CYS cc_start: 0.6788 (OUTLIER) cc_final: 0.5587 (m) REVERT: L 102 GLN cc_start: 0.7714 (mm-40) cc_final: 0.6642 (tp40) REVERT: L 231 GLU cc_start: 0.6623 (pm20) cc_final: 0.4804 (pm20) outliers start: 214 outliers final: 124 residues processed: 478 average time/residue: 0.4143 time to fit residues: 318.5018 Evaluate side-chains 428 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 286 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 413 ASN Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 403 TYR Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 470 CYS Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 150 TYR Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 229 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 397 TYR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 496 ILE Chi-restraints excluded: chain K residue 501 LEU Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 20 TRP Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 234 HIS Chi-restraints excluded: chain L residue 334 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 354 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 225 optimal weight: 0.7980 chunk 283 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 251 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 HIS I 98 ASN ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 GLN K 207 HIS ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 370 ASN ** 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 = 0.4540 r_free = 0.4540 target = 0.115130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.097873 restraints weight = 95236.122| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.34 r_work: 0.4041 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2941 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2995 | |-----------------------------------------------------------------------------| r_final: 0.4036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 32614 Z= 0.271 Angle : 0.784 15.463 44698 Z= 0.401 Chirality : 0.051 0.455 4858 Planarity : 0.006 0.067 5130 Dihedral : 18.319 176.510 5581 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.64 % Favored : 90.08 % Rotamer: Outliers : 7.07 % Allowed : 27.89 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.13), residues: 3466 helix: -1.70 (0.14), residues: 1098 sheet: -2.19 (0.24), residues: 425 loop : -1.96 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 192 HIS 0.011 0.001 HIS K 16 PHE 0.027 0.003 PHE I 419 TYR 0.030 0.002 TYR I 467 ARG 0.006 0.001 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.05574 ( 875) hydrogen bonds : angle 6.22605 ( 2415) covalent geometry : bond 0.00616 (32614) covalent geometry : angle 0.78361 (44698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 289 time to evaluate : 3.222 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: A 16 HIS cc_start: 0.6801 (OUTLIER) cc_final: 0.5174 (p90) REVERT: A 101 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6994 (mt) REVERT: A 225 ARG cc_start: 0.7114 (mpp-170) cc_final: 0.6786 (mpp-170) REVERT: A 373 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7710 (m-10) REVERT: B 44 ASP cc_start: 0.2165 (OUTLIER) cc_final: 0.1921 (m-30) REVERT: B 71 ARG cc_start: 0.6637 (mmt90) cc_final: 0.6424 (mmt90) REVERT: B 122 MET cc_start: 0.7718 (ppp) cc_final: 0.7511 (ppp) REVERT: B 169 GLU cc_start: 0.6244 (mm-30) cc_final: 0.5821 (mm-30) REVERT: B 410 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: C 59 HIS cc_start: 0.7654 (t-90) cc_final: 0.7196 (t-170) REVERT: C 74 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.2941 (ttt) REVERT: C 121 PHE cc_start: 0.5780 (m-80) cc_final: 0.5559 (m-80) REVERT: C 295 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5465 (tpp-160) REVERT: C 358 PHE cc_start: 0.6965 (t80) cc_final: 0.6630 (t80) REVERT: C 501 LEU cc_start: 0.3998 (OUTLIER) cc_final: 0.3745 (mp) REVERT: C 505 TYR cc_start: 0.2937 (OUTLIER) cc_final: 0.1094 (m-80) REVERT: D 89 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6735 (pttp) REVERT: D 260 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6637 (mm-30) REVERT: D 277 MET cc_start: 0.7378 (tpt) cc_final: 0.6843 (tpt) REVERT: D 392 TYR cc_start: 0.7896 (p90) cc_final: 0.7611 (p90) REVERT: I 91 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5176 (mt) REVERT: I 146 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7611 (mm-30) REVERT: I 161 MET cc_start: 0.5008 (ptm) cc_final: 0.4504 (ptp) REVERT: I 224 PHE cc_start: 0.6880 (m-80) cc_final: 0.6114 (m-80) REVERT: I 305 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.5836 (mp) REVERT: I 374 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7078 (mm) REVERT: I 430 GLN cc_start: 0.6176 (OUTLIER) cc_final: 0.5913 (mt0) REVERT: J 14 ASP cc_start: 0.6540 (m-30) cc_final: 0.6308 (m-30) REVERT: J 121 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6250 (mmtt) REVERT: K 141 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8220 (m) REVERT: K 150 TYR cc_start: 0.5021 (OUTLIER) cc_final: 0.4146 (m-10) REVERT: K 506 TYR cc_start: 0.5735 (OUTLIER) cc_final: 0.1956 (m-80) REVERT: L 20 TRP cc_start: 0.1833 (OUTLIER) cc_final: -0.0089 (t60) REVERT: L 34 CYS cc_start: 0.6844 (OUTLIER) cc_final: 0.5672 (m) REVERT: L 45 PHE cc_start: 0.3767 (OUTLIER) cc_final: 0.3378 (p90) REVERT: L 102 GLN cc_start: 0.7823 (mm-40) cc_final: 0.6777 (tp40) REVERT: L 231 GLU cc_start: 0.6644 (pm20) cc_final: 0.4787 (pm20) outliers start: 218 outliers final: 150 residues processed: 469 average time/residue: 0.4235 time to fit residues: 320.3722 Evaluate side-chains 442 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 270 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 413 ASN Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 368 TRP Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 367 HIS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 404 THR Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 470 CYS Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 373 TRP Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 150 TYR Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 397 TYR Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 496 ILE Chi-restraints excluded: chain K residue 501 LEU Chi-restraints excluded: chain K residue 506 TYR Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 20 TRP Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 45 PHE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 234 HIS Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 334 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 286 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN C 98 ASN C 439 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 446 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.117023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.099724 restraints weight = 97387.828| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.63 r_work: 0.4091 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4088 r_free = 0.4088 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2995 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4082 r_free = 0.4082 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3058 | |-----------------------------------------------------------------------------| r_final: 0.4082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32614 Z= 0.162 Angle : 0.678 14.872 44698 Z= 0.345 Chirality : 0.047 0.307 4858 Planarity : 0.005 0.067 5130 Dihedral : 18.035 175.620 5581 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.34 % Favored : 91.37 % Rotamer: Outliers : 5.64 % Allowed : 29.64 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.14), residues: 3466 helix: -1.34 (0.15), residues: 1074 sheet: -2.17 (0.23), residues: 477 loop : -1.79 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 192 HIS 0.006 0.001 HIS B 9 PHE 0.021 0.002 PHE A 210 TYR 0.026 0.001 TYR C 467 ARG 0.005 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 875) hydrogen bonds : angle 5.73124 ( 2415) covalent geometry : bond 0.00363 (32614) covalent geometry : angle 0.67849 (44698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 284 time to evaluate : 3.267 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: A 16 HIS cc_start: 0.6531 (OUTLIER) cc_final: 0.4866 (p90) REVERT: A 101 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6868 (mt) REVERT: A 225 ARG cc_start: 0.7077 (mpp-170) cc_final: 0.6373 (mpp-170) REVERT: B 71 ARG cc_start: 0.6763 (mmt90) cc_final: 0.6470 (mmt90) REVERT: B 122 MET cc_start: 0.7690 (ppp) cc_final: 0.7333 (mmp) REVERT: B 169 GLU cc_start: 0.6343 (mm-30) cc_final: 0.6021 (mm-30) REVERT: B 197 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.5860 (tpt90) REVERT: B 277 MET cc_start: 0.3186 (mpp) cc_final: 0.2811 (mpp) REVERT: B 410 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.5592 (m-10) REVERT: C 59 HIS cc_start: 0.7633 (t-90) cc_final: 0.7247 (t-170) REVERT: C 121 PHE cc_start: 0.6036 (m-80) cc_final: 0.5650 (m-80) REVERT: C 211 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.5908 (mmtt) REVERT: C 358 PHE cc_start: 0.7126 (t80) cc_final: 0.6711 (t80) REVERT: C 505 TYR cc_start: 0.2294 (OUTLIER) cc_final: 0.0460 (m-80) REVERT: D 89 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6611 (pttm) REVERT: D 124 TRP cc_start: 0.4276 (p-90) cc_final: 0.3249 (p-90) REVERT: D 251 TYR cc_start: 0.6411 (t80) cc_final: 0.6187 (t80) REVERT: D 260 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6600 (mm-30) REVERT: D 277 MET cc_start: 0.7436 (tpt) cc_final: 0.6913 (tpt) REVERT: D 392 TYR cc_start: 0.7827 (p90) cc_final: 0.7621 (p90) REVERT: I 91 ILE cc_start: 0.5337 (OUTLIER) cc_final: 0.5027 (mt) REVERT: I 161 MET cc_start: 0.4900 (ptm) cc_final: 0.4385 (ptp) REVERT: I 224 PHE cc_start: 0.6478 (m-80) cc_final: 0.5796 (m-80) REVERT: I 238 PHE cc_start: 0.6327 (p90) cc_final: 0.6037 (p90) REVERT: I 248 ILE cc_start: 0.6779 (tt) cc_final: 0.6510 (mp) REVERT: I 283 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7853 (pp) REVERT: I 374 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7128 (mm) REVERT: I 400 GLU cc_start: 0.5565 (pm20) cc_final: 0.5230 (pm20) REVERT: J 121 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6048 (mmtt) REVERT: K 141 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8186 (m) REVERT: K 358 PHE cc_start: 0.6208 (m-80) cc_final: 0.5841 (m-80) REVERT: L 102 GLN cc_start: 0.7703 (mm-40) cc_final: 0.6619 (tp40) REVERT: L 231 GLU cc_start: 0.6813 (pm20) cc_final: 0.5396 (pm20) REVERT: L 251 TYR cc_start: 0.3968 (t80) cc_final: 0.3171 (t80) outliers start: 174 outliers final: 113 residues processed: 428 average time/residue: 0.4301 time to fit residues: 295.0122 Evaluate side-chains 391 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 265 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 368 TRP Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 367 HIS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 404 THR Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 251 HIS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 362 LYS Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 397 TYR Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 256 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 196 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN C 98 ASN C 439 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.116996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.099539 restraints weight = 97066.471| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.70 r_work: 0.4081 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4078 r_free = 0.4078 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3058 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4074 r_free = 0.4074 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3119 | |-----------------------------------------------------------------------------| r_final: 0.4074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32614 Z= 0.157 Angle : 0.670 13.024 44698 Z= 0.340 Chirality : 0.046 0.314 4858 Planarity : 0.005 0.065 5130 Dihedral : 17.910 176.088 5581 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.31 % Favored : 91.40 % Rotamer: Outliers : 5.48 % Allowed : 29.28 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.14), residues: 3466 helix: -1.21 (0.15), residues: 1083 sheet: -2.02 (0.23), residues: 466 loop : -1.72 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 192 HIS 0.009 0.001 HIS K 251 PHE 0.030 0.002 PHE K 442 TYR 0.023 0.001 TYR C 467 ARG 0.009 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 875) hydrogen bonds : angle 5.58543 ( 2415) covalent geometry : bond 0.00360 (32614) covalent geometry : angle 0.66986 (44698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 273 time to evaluate : 3.132 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: A 16 HIS cc_start: 0.6503 (OUTLIER) cc_final: 0.4870 (p90) REVERT: A 101 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6916 (mt) REVERT: A 210 PHE cc_start: 0.6097 (m-80) cc_final: 0.5431 (m-80) REVERT: A 225 ARG cc_start: 0.7036 (mpp-170) cc_final: 0.6360 (mpp-170) REVERT: B 71 ARG cc_start: 0.6769 (mmt90) cc_final: 0.6473 (mmt90) REVERT: B 122 MET cc_start: 0.7714 (ppp) cc_final: 0.7341 (mmp) REVERT: B 169 GLU cc_start: 0.6359 (mm-30) cc_final: 0.6048 (mm-30) REVERT: B 197 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.5829 (tpt90) REVERT: B 277 MET cc_start: 0.2773 (mpp) cc_final: 0.2399 (mpp) REVERT: B 410 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.5534 (m-10) REVERT: C 59 HIS cc_start: 0.7661 (t-90) cc_final: 0.7252 (t-170) REVERT: C 211 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.5739 (mmtt) REVERT: C 358 PHE cc_start: 0.7145 (t80) cc_final: 0.6765 (t80) REVERT: C 505 TYR cc_start: 0.2140 (OUTLIER) cc_final: 0.0243 (m-80) REVERT: D 89 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6407 (pttm) REVERT: D 124 TRP cc_start: 0.4292 (p-90) cc_final: 0.3216 (p-90) REVERT: D 133 GLU cc_start: 0.8851 (mp0) cc_final: 0.8565 (mm-30) REVERT: D 260 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6689 (mm-30) REVERT: I 56 TYR cc_start: 0.6596 (t80) cc_final: 0.6330 (t80) REVERT: I 91 ILE cc_start: 0.5462 (OUTLIER) cc_final: 0.5101 (mt) REVERT: I 161 MET cc_start: 0.4854 (ptm) cc_final: 0.4324 (ptp) REVERT: I 224 PHE cc_start: 0.6366 (m-80) cc_final: 0.5824 (m-80) REVERT: I 238 PHE cc_start: 0.6397 (p90) cc_final: 0.6011 (p90) REVERT: I 248 ILE cc_start: 0.6760 (tt) cc_final: 0.6469 (mp) REVERT: I 283 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7857 (pp) REVERT: I 374 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7102 (mm) REVERT: I 400 GLU cc_start: 0.5519 (pm20) cc_final: 0.5248 (pm20) REVERT: J 121 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6060 (mmtt) REVERT: K 141 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8187 (m) REVERT: K 358 PHE cc_start: 0.6222 (m-80) cc_final: 0.5860 (m-80) REVERT: K 457 LYS cc_start: 0.5630 (pttm) cc_final: 0.5001 (pttp) REVERT: L 20 TRP cc_start: 0.1329 (OUTLIER) cc_final: -0.0366 (t60) REVERT: L 102 GLN cc_start: 0.7646 (mm-40) cc_final: 0.6416 (tp40) REVERT: L 231 GLU cc_start: 0.6880 (pm20) cc_final: 0.5367 (pm20) outliers start: 169 outliers final: 120 residues processed: 410 average time/residue: 0.4102 time to fit residues: 270.1115 Evaluate side-chains 401 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 267 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 368 TRP Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 367 HIS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 404 THR Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 470 CYS Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 251 HIS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 362 LYS Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 496 ILE Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 20 TRP Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain L residue 198 PHE Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 234 HIS Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 266 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 81 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 319 optimal weight: 0.0370 chunk 173 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 ASN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 468 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.115503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.097863 restraints weight = 97345.565| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.68 r_work: 0.4036 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3119 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3171 | |-----------------------------------------------------------------------------| r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 32614 Z= 0.214 Angle : 0.725 13.650 44698 Z= 0.369 Chirality : 0.048 0.378 4858 Planarity : 0.005 0.068 5130 Dihedral : 17.977 176.492 5581 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.61 % Favored : 90.10 % Rotamer: Outliers : 5.74 % Allowed : 29.41 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 3466 helix: -1.30 (0.15), residues: 1086 sheet: -2.16 (0.23), residues: 480 loop : -1.77 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 192 HIS 0.010 0.001 HIS K 16 PHE 0.027 0.002 PHE K 442 TYR 0.033 0.002 TYR C 467 ARG 0.008 0.001 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 875) hydrogen bonds : angle 5.76656 ( 2415) covalent geometry : bond 0.00490 (32614) covalent geometry : angle 0.72492 (44698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 282 time to evaluate : 3.569 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: A 16 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.5160 (p90) REVERT: A 101 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.7006 (mt) REVERT: A 225 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6715 (mpp-170) REVERT: B 85 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6786 (ptpt) REVERT: B 169 GLU cc_start: 0.6354 (mm-30) cc_final: 0.6077 (mm-30) REVERT: B 197 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.5847 (tpt90) REVERT: B 277 MET cc_start: 0.3080 (mpp) cc_final: 0.2673 (mpp) REVERT: B 410 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.5935 (m-80) REVERT: C 59 HIS cc_start: 0.7769 (t-90) cc_final: 0.7315 (t-170) REVERT: C 74 MET cc_start: 0.3221 (OUTLIER) cc_final: 0.2892 (ttt) REVERT: C 211 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.5578 (mmtt) REVERT: C 358 PHE cc_start: 0.7135 (t80) cc_final: 0.6934 (t80) REVERT: C 505 TYR cc_start: 0.2278 (OUTLIER) cc_final: 0.0102 (m-80) REVERT: D 133 GLU cc_start: 0.8865 (mp0) cc_final: 0.8535 (mm-30) REVERT: D 260 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6549 (mm-30) REVERT: I 91 ILE cc_start: 0.5590 (OUTLIER) cc_final: 0.5185 (mt) REVERT: I 146 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7515 (mm-30) REVERT: I 161 MET cc_start: 0.4768 (ptm) cc_final: 0.4190 (ptp) REVERT: I 224 PHE cc_start: 0.6824 (m-80) cc_final: 0.6016 (m-80) REVERT: I 248 ILE cc_start: 0.6919 (tt) cc_final: 0.6575 (mp) REVERT: I 283 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8034 (pp) REVERT: I 374 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7140 (mm) REVERT: I 400 GLU cc_start: 0.5594 (pm20) cc_final: 0.5331 (pm20) REVERT: J 121 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6063 (mmtt) REVERT: J 309 MET cc_start: 0.5648 (ttt) cc_final: 0.5390 (tpp) REVERT: K 141 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8226 (m) REVERT: K 358 PHE cc_start: 0.6187 (m-80) cc_final: 0.5811 (m-80) REVERT: K 457 LYS cc_start: 0.5662 (pttm) cc_final: 0.5003 (pttp) REVERT: L 20 TRP cc_start: 0.1607 (OUTLIER) cc_final: -0.0139 (t60) REVERT: L 45 PHE cc_start: 0.4140 (OUTLIER) cc_final: 0.3576 (p90) REVERT: L 102 GLN cc_start: 0.7764 (mm-40) cc_final: 0.6610 (tp40) REVERT: L 231 GLU cc_start: 0.7034 (pm20) cc_final: 0.5401 (pm20) outliers start: 177 outliers final: 140 residues processed: 428 average time/residue: 0.4384 time to fit residues: 301.7828 Evaluate side-chains 424 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 267 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 367 HIS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 404 THR Chi-restraints excluded: chain I residue 405 ILE Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 470 CYS Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 251 HIS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 362 LYS Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 454 GLN Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 496 ILE Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 20 TRP Chi-restraints excluded: chain L residue 45 PHE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain L residue 198 PHE Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 234 HIS Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 266 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 67 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.114821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.096719 restraints weight = 96470.232| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.63 r_work: 0.4023 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3171 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3228 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 32614 Z= 0.235 Angle : 0.764 14.947 44698 Z= 0.386 Chirality : 0.050 0.382 4858 Planarity : 0.006 0.066 5130 Dihedral : 18.074 176.160 5581 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.78 % Favored : 89.90 % Rotamer: Outliers : 5.74 % Allowed : 29.70 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.14), residues: 3466 helix: -1.37 (0.15), residues: 1099 sheet: -2.37 (0.22), residues: 487 loop : -1.79 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 192 HIS 0.011 0.001 HIS K 16 PHE 0.028 0.002 PHE K 442 TYR 0.031 0.002 TYR C 467 ARG 0.011 0.001 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 875) hydrogen bonds : angle 5.86457 ( 2415) covalent geometry : bond 0.00537 (32614) covalent geometry : angle 0.76353 (44698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 276 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 HIS cc_start: 0.6632 (OUTLIER) cc_final: 0.5211 (p90) REVERT: A 101 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7029 (mt) REVERT: B 85 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6662 (ptpt) REVERT: B 197 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.5873 (tpt90) REVERT: B 198 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: B 410 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: C 59 HIS cc_start: 0.7785 (t-90) cc_final: 0.7332 (t-170) REVERT: C 74 MET cc_start: 0.3222 (OUTLIER) cc_final: 0.2891 (ttt) REVERT: C 211 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.5575 (mmtt) REVERT: C 358 PHE cc_start: 0.7187 (t80) cc_final: 0.6974 (t80) REVERT: C 407 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6771 (ptt180) REVERT: C 505 TYR cc_start: 0.2283 (OUTLIER) cc_final: 0.0034 (m-80) REVERT: D 133 GLU cc_start: 0.8868 (mp0) cc_final: 0.8560 (mm-30) REVERT: I 91 ILE cc_start: 0.5513 (OUTLIER) cc_final: 0.5116 (mt) REVERT: I 146 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7538 (mm-30) REVERT: I 161 MET cc_start: 0.4779 (ptm) cc_final: 0.4203 (ptp) REVERT: I 224 PHE cc_start: 0.6782 (m-80) cc_final: 0.5998 (m-80) REVERT: I 231 TRP cc_start: 0.7431 (p-90) cc_final: 0.6737 (p-90) REVERT: I 374 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7243 (mm) REVERT: I 400 GLU cc_start: 0.5694 (pm20) cc_final: 0.5423 (pm20) REVERT: J 121 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6024 (mmtt) REVERT: J 309 MET cc_start: 0.5653 (ttt) cc_final: 0.5400 (tpp) REVERT: K 141 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8247 (m) REVERT: K 251 HIS cc_start: 0.4789 (OUTLIER) cc_final: 0.4060 (p90) REVERT: K 457 LYS cc_start: 0.5905 (pttm) cc_final: 0.5277 (pttp) REVERT: L 20 TRP cc_start: 0.1563 (OUTLIER) cc_final: -0.0452 (t60) REVERT: L 45 PHE cc_start: 0.4081 (OUTLIER) cc_final: 0.3497 (p90) REVERT: L 102 GLN cc_start: 0.7913 (mm-40) cc_final: 0.6704 (tp40) REVERT: L 144 VAL cc_start: 0.6028 (m) cc_final: 0.5779 (p) outliers start: 177 outliers final: 139 residues processed: 424 average time/residue: 0.4250 time to fit residues: 291.6433 Evaluate side-chains 421 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 265 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 367 HIS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 404 THR Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 470 CYS Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 251 HIS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 362 LYS Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 496 ILE Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 20 TRP Chi-restraints excluded: chain L residue 45 PHE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain L residue 198 PHE Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 234 HIS Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 72 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 183 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN C 98 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN I 59 HIS I 135 ASN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.116486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.097747 restraints weight = 97319.934| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.73 r_work: 0.4061 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3228 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3277 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32614 Z= 0.158 Angle : 0.702 14.690 44698 Z= 0.353 Chirality : 0.047 0.318 4858 Planarity : 0.005 0.066 5130 Dihedral : 17.971 176.103 5581 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.45 % Favored : 91.23 % Rotamer: Outliers : 4.80 % Allowed : 30.93 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.14), residues: 3466 helix: -1.18 (0.15), residues: 1078 sheet: -2.22 (0.22), residues: 498 loop : -1.70 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 192 HIS 0.005 0.001 HIS K 16 PHE 0.025 0.002 PHE I 206 TYR 0.036 0.002 TYR C 346 ARG 0.007 0.001 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 875) hydrogen bonds : angle 5.59230 ( 2415) covalent geometry : bond 0.00362 (32614) covalent geometry : angle 0.70214 (44698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6932 Ramachandran restraints generated. 3466 Oldfield, 0 Emsley, 3466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 275 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 HIS cc_start: 0.6484 (OUTLIER) cc_final: 0.4852 (p90) REVERT: A 101 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.7017 (mt) REVERT: A 225 ARG cc_start: 0.6958 (mpp-170) cc_final: 0.6634 (mpp-170) REVERT: A 273 ASP cc_start: 0.5292 (OUTLIER) cc_final: 0.3605 (m-30) REVERT: B 85 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6590 (ptpt) REVERT: C 59 HIS cc_start: 0.7714 (t-90) cc_final: 0.7296 (t-170) REVERT: C 74 MET cc_start: 0.3031 (OUTLIER) cc_final: 0.2741 (ttt) REVERT: C 211 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.5722 (mmtt) REVERT: C 505 TYR cc_start: 0.1788 (OUTLIER) cc_final: -0.0209 (m-80) REVERT: D 124 TRP cc_start: 0.4959 (p-90) cc_final: 0.1755 (t-100) REVERT: D 133 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (mm-30) REVERT: D 260 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6677 (mm-30) REVERT: I 91 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5182 (mt) REVERT: I 146 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7531 (mm-30) REVERT: I 161 MET cc_start: 0.4668 (ptm) cc_final: 0.4076 (ptp) REVERT: I 224 PHE cc_start: 0.6489 (m-80) cc_final: 0.5910 (m-80) REVERT: I 248 ILE cc_start: 0.6742 (tt) cc_final: 0.6519 (mp) REVERT: I 283 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8039 (pp) REVERT: I 374 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7065 (mm) REVERT: J 121 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6008 (mmtt) REVERT: J 219 TRP cc_start: 0.6965 (t-100) cc_final: 0.6744 (t-100) REVERT: J 309 MET cc_start: 0.5729 (ttt) cc_final: 0.5510 (tpp) REVERT: K 141 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8177 (m) REVERT: K 248 ILE cc_start: 0.6983 (mt) cc_final: 0.6776 (mp) REVERT: K 251 HIS cc_start: 0.5014 (OUTLIER) cc_final: 0.4202 (p90) REVERT: K 343 LEU cc_start: 0.5880 (tt) cc_final: 0.5634 (tp) REVERT: K 358 PHE cc_start: 0.6207 (m-80) cc_final: 0.5833 (m-80) REVERT: K 457 LYS cc_start: 0.5814 (pttm) cc_final: 0.5213 (pttp) REVERT: L 20 TRP cc_start: 0.1359 (OUTLIER) cc_final: -0.0248 (t60) REVERT: L 102 GLN cc_start: 0.7900 (mm-40) cc_final: 0.6733 (tp40) REVERT: L 144 VAL cc_start: 0.5853 (m) cc_final: 0.5639 (p) REVERT: L 231 GLU cc_start: 0.7216 (pm20) cc_final: 0.5809 (pm20) REVERT: L 309 MET cc_start: 0.6189 (mtt) cc_final: 0.5987 (ppp) outliers start: 148 outliers final: 127 residues processed: 397 average time/residue: 0.4275 time to fit residues: 274.3296 Evaluate side-chains 411 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 268 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 59 HIS Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 242 ILE Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 367 HIS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 404 THR Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 470 CYS Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 217 HIS Chi-restraints excluded: chain K residue 251 HIS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 362 LYS Chi-restraints excluded: chain K residue 405 ILE Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 496 ILE Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 20 TRP Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 196 LYS Chi-restraints excluded: chain L residue 198 PHE Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 234 HIS Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 252 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 326 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 318 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 360 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS I 135 ASN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.115709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.097249 restraints weight = 96473.743| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.68 r_work: 0.4037 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3277 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3311 | |-----------------------------------------------------------------------------| r_final: 0.4037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 32614 Z= 0.185 Angle : 0.722 14.229 44698 Z= 0.364 Chirality : 0.047 0.339 4858 Planarity : 0.005 0.064 5130 Dihedral : 17.992 176.038 5581 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.03 % Favored : 90.68 % Rotamer: Outliers : 4.90 % Allowed : 30.87 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.14), residues: 3466 helix: -1.20 (0.15), residues: 1085 sheet: -2.17 (0.22), residues: 480 loop : -1.72 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 192 HIS 0.008 0.001 HIS K 16 PHE 0.025 0.002 PHE I 206 TYR 0.036 0.002 TYR C 346 ARG 0.009 0.001 ARG I 232 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 875) hydrogen bonds : angle 5.60655 ( 2415) covalent geometry : bond 0.00425 (32614) covalent geometry : angle 0.72207 (44698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17495.00 seconds wall clock time: 302 minutes 53.75 seconds (18173.75 seconds total)